Virology Micro D&R Agam

Essays
ESSAYS:
1. Hepatitis Viruses. Enumerate viruses causing Post – Transfusion hepatitis. Discuss in
detail about the morphology, pathogenesis, laboratory diagnosis and prophylaxis of
Hepatitis B virus (8)
2. Classify rhabdoviruses, details about rabies virus (6)

● SN covered in this: Rabies prophylaxis (5)
3. Classify arbovirus, details about Japanese encephalitis (5)

● SN covered in this: Japanese B encephalitis virus (6)
4. Describe in detail the pathogenesis, laboratory diagnosis, treatment, prevention and

control of dengue fever (5)
● SN covered in this:
i. Dengue fever (3)
ii. Dengue virus (2)
5. DNA viruses. Classify herpes viridae, details about herpes simplex virus, and detail about
Varicella Zoster Virus.
i. Varicella zoster (2)
ii. Human herpes virus
6. Details about EBV (3)

● SN covered in this: EBV (3)
7. Classify picornaviruses. Describe the pathogenesis, clinical features and laboratory

diagnosis of poliovirus. Add a note on prophylaxis against Poliomyelitis. Viruses causing
aseptic meningitis (4)
i. Immune prophylaxis of polio (2)
ii. Lab diagnosis of Poliomyelitis
iii. Aseptic meningitis
8. Describe the morphology of HIV. Describe the pathogenesis and Laboratory diagnosis of
HIV infection. Add a note on pre exposure prophylaxis (2)
● SN covered in this: Laboratory diagnosis of AIDS
9. Discuss briefly on Immunoprophylaxis of viral diseases. Discuss briefly on viral

vaccines.
i. Oral / Sabin polio vaccine (2)
ii. Rabies vaccine (2)
10. Discuss various methods for isolation of viruses in the laboratory.

i. Tissue culture for viruses (4)
ii. Viral inclusion bodies (4)
iii. Cytopathic effects (2)
iv. Viral cell culture
v. Egg culture
11. Describe the morphology, pathogenesis and laboratory diagnosis of Influenza virus.
i. Diagnosis and prophylaxis of H1N1 infection
ii. Recent Swine flu pandemic
iii. Prophylaxis of influenza
iv. Influenza viruses
12. Discuss the pathogenesis, clinical features, complications, laboratory diagnosis of

Rubella virus. Add a note on its prevention.
● SN covered in this: MMR Vaccine (3)
13. Discuss the pathogenesis, clinical features, complications, laboratory diagnosis of

Measles virus. Add a note on its prevention.
i. MMR Vaccine. (3)
ii. Warthin Finkeldey giant cells.(2)
iii. Measles virus (2)
14. Classify Coronaviruses. Discuss the morphology, pathogenesis, clinical features,
laboratory diagnosis, treatment & prevention of COVID-19. Explain in detail the recent
COVID-19 pandemic and other previous outbreaks.
15. Define & Classify Slow virus diseases. Discuss the mechanism, clinical manifestations,
laboratory diagnosis & treatment of Prion diseases. How will you sterilize the Prion
contaminated materials?
● SN covered in this: Slow viruses / slow viral disease of man (2)
16. Classify Paramyxoviruses. Write the morphology, pathogenesis, clinical Features,

laboratory diagnosis, treatment & prevention of Mumps. SN covered in it: Difference
between the orthomyxovirus and paramyxovirus.
ESSAY 1
Hepatitis Viruses. Enumerate viruses causing Post – Transfusion hepatitis. Discuss in detail
about the morphology, pathogenesis, laboratory diagnosis and prophylaxis of Hepatitis B
virus (8)
GENERAL FEATURES OF HEPATITIS VIRUSES

Reference: Essentials of Medical Microbiology, Apurba Sastry E/1: Page No. 527 & 528 Table
no. 50.1
Hepatitis B viruses are:
▪ Most widespread, produces acute self-limiting hepatitis which is subclinical or

symptomatic
▪ Only DNA virus among hepatitis viruses
▪ Belongs to Hepadnaviridae, genus Orthohepadnavirus
MORPHOLOGY:
Three morphologic forms:
1. Spherical forms: Numerous, small (22nm in diameter), made of HBsAg antigen.
2. Tubular or filamentous forms: 22nm diameter, 200 nm long, made of HBsAg antigen
3. Complete form or Dane particles: Large, less frequently observed, 42nm size spherical
virions
Reference: Essentials of Medical Microbiology, Apurba Sastry E/1: Page No. 530 Fig 50.2
PATHOGENESIS:
Mode of replication of HBV
Reference: Essentials of Medical Microbiology, Apurba Sastry E/1: Page No. 532 Fig no. 50.4
CLINICAL MANIFESTATIONS:
Reference: Essentials of Medical Microbiology, Apurba Sastry E/1: Page No. 533 Fig no. 50.5
LABORATORY DIAGNOSIS:
- Definitive diagnosis based on serological demonstration of viral markers
Methods available:
▪ ELISA
▪ Chemiluminescence
▪ ICT
▪ Detection by PCR and quantified by RT PCR
Serological markers of Hepatitis B:
Reference: Essentials of Medical Microbiology, Apurba Sastry E/1: Page No. 534 Fig 50.6
PROPHYLAXIS:
ACTIVE IMMUNIZATION (HEPATITIS B VACCINE):
▪ Method of preparation: HBsAg antigen is used in baker’s yeast by recombinant

technology.
▪ Route of administration: Intramuscular route over deltoid region.
▪ Dosage: 10-20 microgram /dose
30 doses at 0, 3, 6 months
PASSIVE IMMUNIZATION (HEPATITIS B IMMUNOGLOBULIN / HBIG):
▪ Indications: Used immediate protection is required

▪ Timings: HBIG started immediately after accidental exposure.
▪ Recommended dose: 0.06ml / kg single dose by IM
▪ Combined immunization:
Vaccine + HBIG for neonates born to HBV infected mother
GENERAL PROPHYLACTIC MEASURES:
▪ Screening
▪ Safe sex
▪ Safe aseptic surgical practices
▪ Safe injection practices
▪ Health education
ESSAY 2
CLASSIFY RHABDOVIRUSES,
DETAILS ABOUT RABIES VIRUS (6)
SHORT NOTE: RABIES PROPHYLAXIS (5)
RHABDOVIRUSES
▪ Bullet – shaped, enveloped viruses with a single – stranded RNA genome
CLASSIFICATION (Infecting humans)
⮚ Vesiculovirus
⮚ Lyssavirus
Reference: Ananthanarayan and Paniker’s Textbook of Microbiology E/10, Page no. 535, Fig no:
57.1
RABIES VIRUS:
MORPHOLOGY:
● Bullet shaped
● 180 x 75 nm in size
● One end rounded or conical and the other planar or concave.
● Lipoprotein envelope carries knob-like spikes, composed of glycoprotein G. Spikes
may be released by treating with lipid solvents or detergents.
● Beneath the envelope is the membrane or matrix (M) protein layer.
● The core of the virion consists of helically arranged ribonucleoprotein
● The genome is an unsegmented, linear, negative sense RNA.
● RNA-dependent RNA transcriptase and some structural proteins are present in
nucleocapsids.
RESISTANCE:
The virus is sensitive to:
● Ethanol
● Iodine preparations
● Quaternary ammonium compounds
● Soap and detergents
● Lipid solvents (ether, chloroform and acetone)
It is inactivated by:
● Phenol
● Formalin
● beta propionolactone
● Ultraviolet irradiation
● Sunlight
- Thermal inactivation occurs in one hour at 50°C and five minutes at 60°C.
- It dies at room temperature but can survive when stabilised by 50% glycerol for
weeks. It survives at 4°C for weeks.
- It can be preserved at -70°C or by lyophilisation.
- For storage in dry ice, the virus has to be sealed in vials as it is inactivated on
exposure to CO2.
ANTIGENIC PROPERTIES:
GLYCOPROTEIN: The surface spikes are composed of glycoprotein G, important for
pathogenesis, virulence and immunity.
Important properties are:
● It mediates the binding of the virus to acetylcholine receptors in neural tissues.
● It induces hemagglutination inhibiting (HI) antibodies.
● It induces neutralizing antibodies (protective antibodies)
● It stimulates cytotoxic T cell immunity.
● It is a serotype-specific antigen.
● Purified glycoprotein may act as a safe and effective subunit vaccine.
NUCLEOPROTEIN:
Properties of nucleocapsid protein are:
● It induces complement-fixing antibodies.
● The antibodies are not protective.
● The antigen is group specific and cross-reactions are seen with some rabies-related
viruses.
● The antiserum prepared against the nucleocapsid antigen is used in
immunofluorescence tests for diagnostic purpose
● Other antigens identified include two membrane proteins, glycolipid and
RNA-dependent RNA polymerase.
HOST RANGE AND CULTIVATION:

Animals:
● All mammals are susceptible to rabies infection, differences exist in susceptibility
between species.
● Cattle, cats and foxes are highly susceptible
● Skunks, opossums and fowl are relatively resistant.
● Humans and dogs occupy an intermediate position. Pups are more susceptible than adult
dogs.
● Experimental infection can be produced in any laboratory animal
● Mice are the animals of choice. They can be infected by any route. After intracerebral
Inoculation, they develop encephalitis and die within 5-30 days.
Street virus:
● The rabies virus isolated from natural human or animal infection is termed the street
virus.
● Inoculation through any route can cause fatal encephalitis in laboratory animals after a
long and variable incubation period of about 1-12 weeks.
● Intracytoplasmic inclusion bodies (Negri bodies) can be demonstrated in the brain of
animals dying of street virus infection.
● Negri bodies are composed of a finely fibrillar matrix and rabies virus particles and are
most abundant in the cerebellum and hippocampus.
Fixed virus:
● After several serial intracerebral passages in rabbits, the virus undergoes certain changes
and becomes what is called the fixed virus.
● The fixed virus is more neurotropic, though it is much less infective by other routes.
● After intracerebral inoculation, it produces fatal encephalitis after a short and fixed
incubation period of 6-7 days.
● Negri bodies are usually not demonstrable in the brain of animals dying of fixed virus
infection.
● The fixed virus is used for vaccine production.
Chick embryos:
● The rabies virus can be grown in chick embryos.
● The usual mode of inoculation is into the yolk sac.
● Serial propagation in chick embryos has led to the development of attenuated vaccine
strains like Flury and Kelev.
● Strains adapted to duck eggs which give high yields of the virus have been used for
the preparation of inactivated vaccines.
Tissue culture:
● The rabies virus can grow in primary and continuous cell cultures such as chick
embryo fibroblast, and porcine or hamster kidney but cytopathic effects are not
apparent and the yield of virus is low.
● The fixed virus strains adapted for growth in human diploid cell, chick embryo and
Vero cell cultures are used for the production of vaccines.
RABIES
● Rabies has been recognized since ancient times as a disease transmitted to humans and
animals by the bite of 'mad dogs'.
● The disease in human beings is called hydrophobia because the patient exhibits fear of
water, being incapable of drinking though subject to intolerable thirst.
● The causative agent has been associated with the saliva of rabid dogs.
● In a series of studies from 1881, Pasteur established that the rabies virus was present in
the brain of infected animals. By serial intracerebral passage in rabbits, he obtained the
fixed virus and demonstrated that dogs could be rendered immune by a series of
injections of fixed virus of graded infectivity.
● This vaccine was prepared by drying, for various periods, pieces of spinal cord from
rabbits infected with the fixed virus.
● In July 1885, Joseph Meister, a nine-year-old boy, severely bitten by a rabid dog and was
risk of developing rabies, was given a course of 13 inoculations of the infected cord
vaccine by Pasteur.
● The boy survived, this event was a milestone in the development of medicine.
PATHOGENICITY:
Reference: Ananthanarayan and Paniker’s Textbook of Microbiology E/10, Page No. 536; Fig
57.2
CLINICAL STAGES:
STAGES OF DISEASE IN HUMANS:
1. Prodrome: (Early stage of this disease)

● The symptoms are fever, headache, malaise, fatigue, and anorexia.
● An early symptom is often a neuritic type of pain or paresthesia and fasciculation at the
site of virus entry.
● Apprehension, anxiety, agitation, irritability, nervousness, insomnia and depression
characterize the prodromal phase, which usually lasts 2-4 days.
2. Acute encephalitic phase: (Acute neurological phase)
● Begins with hyperactivity characteristically intermittent, with bizarre behavior, agitation
or seizures appearing between apparently normal periods
● The pathognomonic feature is difficulty in drinking with intense thirst.
● Patients may be able to swallow dry solids but not liquids.
● Attempts to drink bring on such painful spasms of the pharynx and larynx, producing
choking or gagging.
● The patients may fear even the sight or sound of water (hydrophobia).
● Generalized convulsions follow
3. Coma
4. Death occurs within 1-6 days due to respiratory arrest during convulsions.
STAGES OF DISEASE IN DOGS:

● In dogs, the incubation period is usually 3 – 6 weeks but may range from 10 days to a
year.
● The initial signs are troubled air and a change in disposition with restlessness, snapping at
imaginary objects, licking at the site of the bite.
● After 2-3 days of this prodromal stage, the disease develops into either the furious or
dumb type of rabies.
1. Furious rabies, which is more common, the dog runs amok, biting without
provocation and indiscriminately.
▪ The lower jaw droops and saliva drools from the mouth. Paralysis,
convulsions and death follow.
2. Dumb rabies is the paralytic form in which the animal lies huddled, unable to
feed.
▪ The dog may not bite but attempts to feed it are dangerous.
▪ The dumb form is as infectious as the furious type.
▪ Rabid dogs usually die in 3 – 5 days.
i. SPECIMEN: Corneal smears and skin biopsy (from face or neck) or saliva antemortem,
and brain postmortem.
ii. DIRECT MICROSCOPY:
● Antemortem: Commonly used for diagnosis is the demonstration of rabies virus antigens by
immunofluorescence.
▪ Direct immunofluorescence is done using monoclonal antibodies tagged with
fluorescein isothiocyanate.
▪ Immunoperoxidase staining can be used in to antigen in tissues.
● Postmortem: Diagnosis may be made postmortem by demonstration of Negri bodies in the
brain, but they may be absent in about 20 % of cases.
ISOLATION:
i. Animal inoculation: Isolation of the virus by intracerebral inoculation in mice can be
attempted from the brain, CSF, saliva and urine (biological test).
● Chances of isolation are greater early in the disease
● A few days after onset, neutralizing antibodies appear and the virus can then be isolated
only occasionally
ii. Tissue culture: A more rapid and sensitive method is isolation of the virus in tissue
culture cell lines (WI 38, BHK 21, CER).
● CPE is minimal and so virus isolation is identified by immunofluorescence.
● A positive IF test can be obtained as early as 2 – 4 days after inoculation.
● The identity of the isolate can be established by the neutralization test with specific anti
rabies antibody.
iii. Antibody demonstration: High titre antibodies are present in the CSF in rabies but not
after immunisation.
iv. Molecular methods: Detection of rabies virus RNA by reverse transcription PCR is a
sensitive method.
RABIES PROPHYLAXIS
PRE – EXPOSURE:
● In animals, this is imperative but human pre – exposure immunization was only used in
persons at high risk, such as veterinarians and dog handlers because neural vaccines
carry some risk of serious complications .
● The introduction of cell culture vaccines, which are free from serious complications,
has made pre – exposure immunization in humans safe and feasible.
POST EXPOSURE:
● Specific prophylaxis is generally used after exposure to infection and is therefore called
antirabic treatment.
This consists of
1. Local treatment
2. Active immunization with antirabic vaccines
3. Passive immunization with antirabies serum.
Local treatment: Animal bites deposit the virus in the wound. Prompt cauterisation of the
wound therefore helps destroy the virus.
● The wound should be scrubbed well immediately with soap and water. This is a very
important step in the prevention of rabies as soap destroys the virus effectively.
● After washing the soap away completely, the wound is treated with quaternary
ammonium compounds (such as cetavlon), tincture or aqueous solution of iodine, or
alcohol (40-70%).
● Antirabic serum may be applied topically and infiltrated around the wound.
Antirabic vaccines:
These fall into two main categories:
1. Neural (associated with serious risk of neurological complications and are no longer
used)
2. Non – neural
1. Neural vaccines:
Semple vaccine: This vaccine developed by Semple (1911) at the Central Research Institute,
Kasauli (India) was the most widely used vaccine.
● It is a 5% suspension of sheep brain infected with fixed virus and inactivated with phenol
at 37°C, leaving no residual live virus.
Beta propionolactone (BPL) vaccine: Modified form of the Semple vaccine, in which beta
propiolactone is used as the inactivating agent instead of phenol.
● It is believed to be more antigenic, so smaller doses are considered adequate.
● The major antirabic vaccine producing laboratories in India manufacture BPL vaccine.
Suckling mouse brain vaccines: The encephalitogenic factor in brain tissue is a basic protein
associated with myelin.
● It is scanty or absent in the non – myelinated neural tissue of newborn animals.
● So vaccines were developed using infant mouse, rat or rabbit brains.
● It is impractical in India as very large quantities are required.
2. Non – neural vaccines:

Egg vaccines:
Duck egg vaccine
● Prepared from a fixed virus adapted for growth in duck eggs and inactivated with beta
propiolactone, but was discontinued due to poor immunogenicity.
● A purified, more potent duck egg vaccine was developed, but was supplanted by tissue
culture vaccines which became available then.
Live attenuated chick embryo vaccines: (not in use now)
Two types of vaccines were developed with the Flury strain:
A. Low Egg Passage (LEP) vaccine at 40-50 egg passage level for immunization of dogs.
B. High Egg Passage (HEP) vaccine at 180 passage level for cattle and cats.
TISSUE CULTURE VACCINES:

● Human diploid cell (HDC) vaccine:
▪ The first cell culture vaccine
▪ Developed by Koprowsky, Wiktor and Plotkin.
▪ It is a purified and concentrated preparation of fixed rabies virus (Pitman- Moore
strain)
▪ Grown on human diploid cells (WI 38 or MRC5) and inactivated with beta
propiolactone or tri-n-butyl phosphate
▪ highly antigenic
▪ Free from serious side effects.
⮚ Disadvantage - its high cost.
● Other equally effective and more economical vaccines have been developed ,they are
1. Primary cell culture vaccines grown on chick embryos.
2. Continuous cell culture vaccines grown on the Vero cell line of the monkey kidney
● Cell culture vaccines are available in India are:
1. Human diploid cell (HDC) vaccine
2. Purified chick embryo cell (PCEC) vaccine
3. Purified Vero cell (PVC) vaccine
● All three of them are equally safe and effective. These are currently used for
immunization.
ESSAY 3
CLASSIFY ARBOVIRUS, DETAILS ABOUT JAPANESE ENCEPHALITIS (5)
SHORT NOTE: JAPANESE B ENCEPHALITIS VIRUS (6)
ARBOVIRUSES
▪ Arthropod - borne viruses
▪ RNA viruses
▪ Transmitted by blood sucking arthropods from one vertebrae host to another
▪ They multiply inside the insects
CLASSIFICATION:
● Has 5 different families
▪ Togaviridae
▪ Flaviviridae
▪ Bunyaviridae
▪ Reoviridae
▪ Rhabdoviridae
Some examples of Arbovirus:
Virus Manifestation Distribution Vector Reservoir
Family: Togaviridae
Chikungunya Fever, arthritis Asia, Africa Aedes aegypti Monkeys

virus
Eastern equine Encephalitis East part of Aedes, Culex Birds

encephalitis North America
virus
Family: Flaviviridae
Japanese B Encephalitis South East Asia Culex Pigs, birds

encephalitis tritaeniorhynchu
s
Dengue virus Hemorrhagic India Aedes aegypti -
fever
Yellow fever Hemorrhagic West Africa Aedes aegypti Monkeys

virus fever
Kyasanur forest Hemorrhagic Russia Tick Monkeys and rat

disease virus fever
Zika virus Fever and Brazil Aedes aegypti Monkeys

arthritis
Family: Bunyaviridae
California Encephalitis USA Aedes triseriatus Rodents

encephalitis
virus
Family: Reoviridae
Colorado tick Fever, rarely America Tick Rodents

fever virus encephalitis
Family: Rhabdoviridae
Chandipura virus Encephalitis India Sand fly -
JAPANESE ENCEPHALITIS
● Belongs to family Flaviviridae
● Enveloped virus
● Contain ss RNA
EPIDEMIOLOGY:
● Vector
▪ Transmitted by bite of Culex mosquito (C. tritaeniorhynchus)
● Transmission cycle
▪ Infects several non human hosts e.g. animals and birds
▪ Animal hosts – pigs, cattle, horses and humans
▪ Bird hosts – Ardeid birds
▪ Humans are considered as dead end
(Pigs → Culex → pigs)
(Ardeid birds → Culex → Ardeid birds)
● Age
▪ Most cases are common in children below 15 years (but infants are not affected)
● Incubation period: 5-15 days
● Subclinical infection is common - It shows the iceberg phenomenon.
● Clinical course is divided into three stages:
1. Prodromal stage: Febrile illness; the onset of which maybe either abrupt, acute
or subacute (commonly)
2. Acute encephalitis stage: Characterized by acute onset of fever, mental
confusion, disorientation, delirium, seizures, or coma
3. Late stage and sequelae: Patient may be fully recovered or retain some
neurological deficits permanently (Case fatality 20-40%)
▪ IgM capture antibody ELISA
▪ RT PCR
TREATMENT:
- Only supportive measures and no specific antiviral drugs are available.
PREVENTION:
● Children residing in rural areas and individuals living in endemic areas are recommended
to take vaccines.
● Vaccines licensed in India are:
▪ Live attenuated SA 14-14-2 vaccine
▪ Inactivated JE vaccine
▪ Catch up vaccination
▪ Combined vaccine
ESSAY 4
DESCRIBE IN DETAIL THE PATHOGENESIS, LABORATORY DIAGNOSIS,
TREATMENT, PREVENTION AND CONTROL OF DENGUE FEVER (5)
SHORT NOTE: DENGUE VIRUS
DENGUE VIRUS
▪ Most common arbovirus found in India.
▪ Has four serotypes (DEN-1 to DEN-4). Recently, the fifth serotype (DEN-5) was
discovered in 2013 from Bangkok. It is also called break-bone fever.
▪ Dengue virus can be detected in blood from 1 day before the onset of symptoms up to 5
days thereafter.
VECTOR:
Aedes aegypti is the principal vector followed by Aedes albopictus. They bite during the day
time.
● Aegypti is a nervous feeder (so, it bites repeatedly to more than one person to complete a
blood meal) and resides in domestic places, hence is the most efficient vector.
● Aedes albopictus is found in peripheral urban areas. It is an aggressive and concordant
feeder i.e. can complete its blood meal in one go; hence is less efficient in transmission.
● Aedes becomes infective only when it feeds on viremic patients (generally from a day
before to the end of the febrile period i.e. 5 days.)
● Extrinsic incubation period of 8-10 days is needed before Aedes to become infective.
However, once infected, it remains infectious for life.
● Aedes can pass the dengue virus to its offspring; by transovarial transmission.
● Transmission cycle: Man and Aedes are the principal reservoirs. Transmission cycle does
not involve other animals.
PATHOGENESIS:
● Primary dengue infection occurs when a person is infected with dengue virus for the first
time with any one serotype.
● Months to years later; a more severe form of dengue illness may appear (called secondary
dengue infection) due to infection with another second serotype which is different from
the first serotype causing primary infection.
● Infection with dengue virus induces the production of neutralizing and non-neutralizing
antibodies.
● The neutralizing antibodies are protective in nature. Such antibodies are produced
against the infective serotype (which lasts lifelong) as well as against other serotypes
(which last for some time). Hence, protection to infective serotypes stays lifelong but
cross protection to other serotypes diminishes over a few months.
● The non-neutralizing antibodies last lifelong and are heterotypic in nature; i.e they are
produced against other serotypes but not against the infective serotype. Such antibodies
produced following the first serotype infection, can bind to a second serotype; but instead
of neutralizing the second serotype, it protects it from the host immune system by
inhibiting the bystander B cell activation against the second serotype. This is called
antibody dependent enhancement (ADE) which explains the reason behind the severity
of secondary dengue infection. Among all the serotype combinations, ADE is remarkably
observed when serotype 1 infection is followed by serotype 2, which also claims to be the
most severe form of dengue infection.
1. NS1 Antigen Detection:
ELISA and ICT formats are available for detecting NS1 antigen in serum. They gained
recent popularity because of the early detection of the infection.
● NS1 antigen becomes detectable from day 1 of fever and remains positive up to
18 days.
● Highly specific: It differentiates between flaviviruses. It can also be specific to
different dengue serotypes.
2. Antibody Detection:
● In primary infection: Antibody response is slow and of low titer. IgM appears
first after 5 days of fever and disappears within 90 days. IgG is detectable at low
titer in 14-21 days of illness, and then it slowly increases.
● In secondary infection: IgG antibody titers raise rapidly. IgG is often cross
reactive with many Flaviviruses and may give false positive result after recent
infection or vaccination with yellow fever virus or JE. In contrast, IgM titer is
significantly low and may be undetectable.
● In past infection: Low levels of IgG remain detectable for over 60 years and, in
the absence of symptoms, is a useful indicator of past infection.
● MAC-ELISA is the most recommended tool available currently for dengue
infection. It has a sensitivity and specificity of approximately 90% and 98%
respectively.
● Formats are available for detection of both IgM and IgG separately.
● Rapid tests such as dipstick assays are also available.
● Other antibody detection assays used previously are:
a) HAJ (Hemagglutination inhibition test)
b) CFT (Complement fixation test)
c) Neutralization tests such as plaque reduction test, neutralization and micro
neutralization tests.
3. Virus Detection
Dengue virus can be detected in blood from 1 day before the onset of symptoms upto 5
days thereafter.
● Virus isolation can be done by inoculation into mosquito cell lines or in mice.
● Detection of specific genes of viral RNA by real time RT PCR. It is the most
sensitive and specific assay, can be used for detection of serotypes and
quantification of viral load in blood.
DENGUE FEVER
▪ Acute febrile illness with two or more of the following manifestations: Headache,
retro-orbital pain, myalgia, arthralgia, rash, rubelliform exanthema, hemorrhagic
manifestations.
▪ Dengue manifests after an incubation period of 3-14 days. This acute febrile phase
usually lasts 2 – 7 days.
It is characterized by:
● Abrupt onset of high fever (also called biphasic fever, break bone fever or saddle back
fever).
● Skin erythema and pain in the back and limbs (break-bone fever)
● Maculopapular rashes over the chest and upper limbs.
● Severe frontal headache.
● Muscle and Joint pains
● Lymphadenopathy
● Retro orbital pain
● Loss of appetite, nausea and vomiting
● Photophobia, accompanied by facial flushing
Dengue hemorrhagic fever (DHF): These patients become worse around the time of
defervescence, when the temperature drops to 37.5-38°C or less and remains below this level,
usually on days 3-8 of illness. It is characterised by clinical criteria of dengue fever plus
hemorrhagic tendencies evidenced by one or more of the following:
● Positive tourniquet test (>20 petechial spots per square inch area in cubital fossa.
● High grade continuous fever
● Petechiae, ecchymoses or purpura
● Bleeding from mucosa, gastrointestinal tract. injection sites or other sites
● Raised hematocrit (packed cell volume) by 20%
● Thrombocytopenia (platelet count < l Lakh/mm3)
● Hepatomegaly
● Signs of plasma leakage (pleural effusion, ascites, hypoproteinemia)
Dengue shock syndrome (DSS): All the above criteria for DHF with evidence of circulatory
failure manifested by rapid and weak pulse and narrow pulse pressure (< 20 mm Hg) or
hypotension for age, cold and clammy skin and restlessness.
PREVENTION AND CONTROL:
Vaccine: While no licensed dengue vaccine is available, several vaccine trials are currently being
evaluated.
● Live-attenuated tetravalent vaccine based on chimeric yellow fever-dengue virus

(CYD-TDV) has been developed by Sanofi Pasteur Company.
● Mosquito control measures.
TREATMENT:
▪ There is no specific treatment for dengue.
▪ Supportive management, with cold tepid sponging, paracetamol for fever (Aspirin/
NSAIDS like Ibuprofen, etc., should be avoided since it may cause gastritis, vomiting,
acidosis, platelet dysfunction and severe bleeding); fluid and electrolyte replacement and
platelet infusion when counts are 10,000 and less, should be done.
▪ Dengue shock is treated with whole blood transfusion and management of shock.
ESSAY 5
DNA VIRUSES. CLASSIFY HERPES VIRIDAE, DETAILS ABOUT HERPES SIMPLEX
VIRUS, DETAIL ABOUT VARICELLA ZOSTER VIRUS.
SHORT NOTE: VARICELLA ZOSTER (2)
HUMAN HERPES VIRUS

DNA viruses include:
▪ Herpes viruses
▪ Pox viruses
▪ Parvoviruses
▪ Human papillomaviruses
Herpes viridae consists of a group of viruses which establish latent or persistent infections in
their hosts and later on undergo periodic reactivation.
CLASSIFICATION:
Family- "Herpesviridae"
SUBFAMILY GENUS SPECIES

("herpesvirinae")
Official name Common name
Alpha Simplex virus Human herpesvirus 1 Herpes simplex virus

type 1
Human herpesvirus 2 Herpes simplex virus

type 2
Varicellovirus Human herpesvirus 3 Varicella-zoster virus
Beta Cytomegalovirus Human herpesvirus 4 Cytomegalovirus
Roseolovirus Human herpesvirus 5 Human herpesvirus 6
Human herpesvirus 6 Human herpesvirus 7
Gamma Lymphocryptovirus Human herpesvirus 7 Epstein-barr virus

Rhadinovirus Human herpesvirus 8 Kaposi's sarcoma
associated
herpesvirus
MORPHOLOGY:
▪ Large, spherical in shape
▪ Linear ds DNA
▪ Icosahedral symmetry
▪ Nucleocapsid is surrounded by lipid envelope inserted with glycoprotein spikes
▪ Tegument – between capsid and envelope
Reference: Essentials of Medical Microbiology, Apurba Sastry E/3 Page No. 550, Fig. 56.1
HERPES SIMPLEX VIRUS

▪ Belong to alpha subfamily of herpes viridae
▪ Replicate fast, spread fast
▪ Cytolytic
▪ Undergo latency in nerve cells and reactivate later causing recurrent lesions
▪ They are of two types HSV-1 and HSV-2
PATHOGENESIS:
HERPES SIMPLEX VIRUS 1 HERPES SIMPLEX VIRUS 2
Transmission occurs through Transmission occurs through

● Oropharyngeal contact with infected ● Sexual contact
saliva ● Vertical mode rarely (from mother to
● Direct skin contact foetus)
Latency in trigeminal ganglia Latency in sacral ganglia
Young children are affected Young adults are affected
Skin lesions – above the waist Skin lesions – below the waist
(Most common site of infection – around (Most common site of infection – genital
mouth) area)
RECURRENT INFECTIONS:
Provocative stimuli (fever, axonal injury, UV rays, physical or emotional stress)
⬇️
Reactivation of the latent virus
⬇️
Via axonal spread
⬇️
Back to peripheral site and further replicates in skin and mucosa producing secondary lesions
Recurrent infections are less extensive and severe
Incubation period: 1 to 26 days
❏ Oral- facial mucosal lesions
➔ Gingivostomatitis and pharyngitis
➔ Herpes labialis (painful vesicles near lips)
➔ Tonsillitis and vesicular lesions on the eyelids
❏ Cutaneous lesions
➔ Herpetic Whitlow
➔ Febrile blisters
➔ Eczema herpeticum
➔ Erythema multiforme
➔ Herpes gladiatorial
❏ Genital lesions
➔ Bilateral, painful, multiple, tiny vesicular ulcers
❏ CNS infections
➔ Encephalitis, meningitis, Bell's palsy
❏ Ocular manifestations
➔ Keratoconjunctivitis, corneal ulcer and blindness
❏ Visceral and disseminated herpes
➔ Pneumonitis, tracheobronchitis and hepatitis
❏ Neonatal herpes
➔ Transmitted more commonly during birth than in utero. Always symptomatic.
EPIDEMIOLOGICAL PATTERN:
HSV-1:
● Primary infection occurs early in life and is a either asymptomatic or remains confined to
oropharyngeal disease
● Antibodies develop but they fail to eliminate the virus from the body
HSV-2:
● Primary infection occurs in adult life.
● Antibodies develop only in less number of people
▪ Cytopathology (Tzanck preparation)
▪ Viral antigen detection in specimen by direct IF
▪ HSV DNA detection by PCR
▪ Antibody detection by ELISA
TREATMENT:
▪ Acyclovir is the drug of choice.
▪ It acts by inhibiting viral DNA polymerase.
PREVENTION:
▪ Use of condom to prevent genital herpes
▪ Neonatal herpes can be prevented by prior administration of acyclovir to the mother
during third trimester of pregnancy or delivery by elective Caesarean section
VARICELLA – ZOSTER VIRUS INFECTIONS

- Varicella – zoster virus produces vesicular eruptions (rashes) on the skin and the mucous
membrane in the form of:
● Chicken pox
● Zoster or shingles
CHICKEN POX
- Generalized diffuse bilateral vesicular rashes which occur following primary infection
usually affecting children.
PATHOGENESIS:
Virus enters through the upper respiratory mucosa or the conjunctiva by
● Aerosol ( most common)
● Contact transmission
Infected mononuclear cells in blood carried from local site to the target sites like
● Skin (rashes)
● Respiratory tract (shed in respiratory secretions)
● Neurones (undergoes latency)
● Incubation period- 10-21 days
● Rashes
▪ Rashes are vesicular
▪ Centripetal, bilateral and diffuse in distribution
▪ Rashes appear in multiple crops
▪ Fever appears with each crop of rashes
● Chickenpox in adults causes more severe Bulbous and hemorrhagic rashes leaving behind
pitted scars on skin after recovery.
COMPLICATIONS:
Seen more common in adults and in immunocompromised individuals
▪ Secondary bacterial infections of the skin
▪ Cerebellar ataxia, encephalitis in children
▪ Varicella pneumonia (common in adults)
▪ Nephritis, arthritis and myocarditis.
Chickenpox in pregnancy can affect both mother and the foetus
● Mothers are at high risk of developing Varicella pneumonia
● Foetus is at higher risk of developing congenital Varicella syndrome
ZOSTER OR SHINGLES
Occurs due to reactivation of latent Varicella zoster virus
● In old age (above 60 years)
● In immunocompromised individual
● Occasional in healthy adults
▪ Severe pain in area of skin or mucosa supplied by ganglia
▪ Rashes of unilateral, segmental confined to the area of skin supplied by affected nerve
▪ Ophthalmic branch of trigeminal nerve is the most common nerve involved
COMPLICATIONS OF ZOSTER:
▪ Zoster ophthalmicus (unilateral painful crops of skin rashes around eyes)
▪ Post herpetic neuralgia (pain at local site lasting for months)
▪ Ramsay hunt syndrome (when geniculate ganglion of facial nerve is affected)
▪ Pneumonia
▪ Cytopathology
▪ Specimen collection from lesions
▪ Virus isolation
▪ Varicella zoster specific gene detection by PCR
▪ Specific IgM and IgG antibody detection by ELISA
▪ Specific antigen detection by direct immunofluorescence staining
TREATMENT:
● Acyclovir, Famciclovir or Valacyclovir are the drugs of choice.
PREVENTION:
▪ Live attenuated vaccine using Oka strain of Varicella zoster is given to children after one
year of age.
▪ Varicella-Zoster immunoglobulin is useful for post exposure prophylaxis within 96 hours
of exposure in
● Adults at higher risk of Varicella related death
● Neonates born to mother suffering from chickenpox
▪ Isolation of patients infected with Varicella zoster virus.
ESSAY 6
DETAILS ABOUT EBV
SHORT NOTE: EBV
EPSTEIN – BARR VIRUS

▪ Member of the gamma sub-family of Herpesviridae that causes infectious mononucleosis.
▪ Also associated with several human tumors, including nasopharyngeal carcinoma,
Burkitt's lymphoma, Hodgkin's disease and B cell lymphoma.
ANTIGENS OF EBV:
Divided into three classes:
• Latent phase antigens: They are synthesized during the period of latency, e.g., EBV nuclear
antigen (EBNA): II has six subtypes, Latent membrane protein (LMP): II has two subtypes.
• Early antigens: They are non-structural proteins which help in viral replication.
• Late antigens: they are the structural proteins that form viral capsid and envelope.
PATHOGENESIS:
Primary Infection
EBV is transmitted by oropharyngeal contact through infected salivary secretions.
▪ EBV receptors: EBV binds to specific receptors present on B cell (CD21 or CR2) which
are also receptors for C3b component of complement. Such receptors are also present on
pharyngeal epithelial cells.
▪ Primary infection occurs in the oropharynx. EBV replicates in epithelial cells surface B
lymphocytes of the pharynx and salivary glands.
▪ Following entry into the B cells, EBV directly enters into the latent phase without
completing the viral replication.
▪ Though, majority of the infected cells are eliminated, a small number of infected cells
(one in 10"- 10" B cells) may persist for lifetime. Virus spreads from the oropharynx to
other sites of the body and is capable of undergoing reactivation later.
▪ Viral shedding continues in oropharyngeal secretions at low levels for weeks to months
and serves as a source of infection.
▪ In children, most primary infections are subclinical, but young adults often develop a
condition called acute infectious mononucleosis. Infected B cells become immortalized
by the virus and synthesize large number of variety of immunoglobulins (polyclonal),
many of those are autoantibodies (e.g., heterophile antibody to sheep RBC antigen) In
response to this, the bystander CD8 T Lymphocytes are stimulated and appear atypical.
1. Infectious Mononucleosis
2. EBV-associated Malignancies
3. Lymphoproliferative disorder (seen among immunodeficient patients, e.g. Duncan

syndrome which is an X-linked recessive disease affecting young boys.)
4. Hairy cell leukoplakia (Wart-like growth of epithelial cells of die tongue developed in
some HIV-infected patients and transplant recipients )
5. Chronic fatigue syndrome
INFECTIOUS MONONUCLEOSIS (KISSING DISEASE):
▪ Age: Young adults of developed countries are usually affected.

▪ It is characterized by:
● Headache, fever, malaise
● Pharyngitis
● Cervical lymphadenopathy
● Hepatosplenomegaly
● Rashes following ampicillin therapy
● Atypical lymphocytosis (CD8 T cells)
● Autoantibodies reactive to sheep RBC antigen (detected by Paul Bunnell test)
EBV-ASSOCIATED MALIGNANCIES:
1. Burkitt's lymphoma (tumor of the jaw seen in children and young adults): EBV is
associated with 90% of African and 20% of non-African cases of Burkitt's lymphoma.
▪ Most of the cases have pre-existing mutation {t(8;14)}
▪ Falciparum malaria may impair host CMI and stimulate the EBV-infected B cells.
2. Nasopharyngeal Carcinoma: It is seen among Chinese people who have a history of

intake of salted fish (nitrosamine) and herbal snuff (phorbol ester).
3. Hodgkin’s lymphoma: (especially the mixed – cellularity type): EBV DNA is found in
Reed-Sternberg cells, in atleast50% of cases of Hodgkin’s lymphoma.
4. NHL (Non-Hodgkin's lymphoma): All central nervous system non-Hodgkin's
lymphomas and 50% of systemic non-Hodgkin's lymphomas are EBV positive.
EPIDEMIOLOGY:
▪ Worldwide in distribution:
▪ Age: EBV infections are most common in early childhood, with a second peak during
late adolescence. However, infectious mononucleosis is common among young adults of
developed countries.
▪ Prevalence: EBV is common in all parts of the world, with > 90% of adults being
seropositive and develops antibodies to EBV.
▪ Transmission: Intimate and prolonged oral contact is required for effective transmission.
- EBV is spread by direct contact with oral secretions, e.g. salivary contact during kissing
- Other modes are blood transfusion and following bone marrow transplantation.
- Source: Asymptomatic seropositive individuals shed the virus in oropharyngeal
secretions. Shedding is more in immuno-compromised patients
Antibody Detection: Heterophile Agglutination Test
▪ Paul-Bunnell test: It is a tube agglutination test that uses sheep RBCs to detect
heterophile antibodies in a patient's serum.
▪ Procedure: Serial dilutions of inactivated (56°C for30 minutes) patient's serum are mixed
with equal volumes of 1 % sheep RBC's and then the tubes are incubated at 37°C for four
hours.
▪ Result: Agglutination titre of > 256 is considered as significant.
▪ False positive: Heterophile antibodies are non-specific, may also be present following
serum therapy or even in some normal individuals; hence confirmation is must.
▪ Differential absorption is done for confirmation.
▪ Patient's serum is first made to react with guinea pig kidney cells and ox red cells,
following which the Paul-Bunnell test is repeated.
▪ Monospot test is modified heterophile agglutination test is available commercially.
● It is a simple slide agglutination test that uses horse RBCs instead of sheep
RBCs.
● Test serum is priorly treated with guinea pig kidney and ox red cells.
● It has largely replaced the differential absorption test, and has excellent
sensitivity (75%) and specificity (90%).
▪ Heterophile antibodies appear early (40% in the first week and 80- 90% in the third week
of illness), then disappear within 3 months.
▪ Heterophile antibodies are not detectable in children < 5 years, in elderly or in patients
with atypical symptoms.
PREVENTION:
The isolation of patients with infectious mononucleosis is not needed as temporary contact does
not transmit the infection. No vaccine is currently available. A vaccine trial using EBV
glycoprotein was found to be ineffective.
ESSAY 7
CLASSIFY PICORNAVIRUSES. DESCRIBE THE PATHOGENESIS, CLINICAL FEATURES
AND LAB DIAGNOSIS OF POLIOVIRUS. ADD A NOTE ON PROPHYLAXIS AGAINST
POLIOMYELITIS. VIRUSES CAUSING ASEPTIC MENINGITIS.
SHORT NOTES:
i. IMMUNE PROPHYLAXIS OF POLIO
ii. LAB DIAGNOSIS OF POLIOMYELITIS
iii. ASEPTIC MENINGITIS
PICORNAVIRUSES
MAJOR GROUPS:
● Enteroviruses
● Rhinoviruses
Enteroviruses:
▪ Transmission- Feco oral route
▪ Doesn't cause intestinal manifestation
▪ > 115 human serotype
CLINICAL MANIFESTATIONS OF VARIOUS VIRUSES:

● Polio viruses – meningitis
● Coxsackie viruses( B,A7,A9) – aseptic meningitis
● Echo viruses – aseptic meningitis
● Parechoviruses – aseptic meningitis
● Enteroviruses 71 – aseptic meningitis
● Enterovirus 68 – pneumonia
● Enterovirus 70 – acute hemorrhagic conjunctivitis
● Enterovirus 72 – reclassified into hepatitis A virus
POLIOVIRUS
- Causes a highly infectious childhood disease called Polio / poliomyelitis causing acute
flaccid paralysis due to involvement of the nervous system.
MORPHOLOGY:
▪ Type of Enterovirus (Family: Picornaviridae)
▪ Size: 28-30nm
▪ Shape: Spherical
▪ Symmetry: Icosahedral
▪ Envelope: non enveloped
▪ Capsid: Composed of 60 subunits (capsomeres)
o Each capsomeres has 4 viral proteins (VP1-VP4)
o Each parechoviruses - 3 proteins
▪ Nucleic acid: single stranded +ve sense linear RNA
ANTIGENIC TYPES:
● Wild polioviruses (WPV) – Cause natural disease
● Vaccine derived polioviruses (VDPV) - These are vaccine strains which regained
neurovirulence and produce diseases in man
SITE OF ACTION:
- Motor nerve ending (i.e. anterior horn cells of spinal cord) and leads to muscle weakness
and flaccid paralysis
NEURON DEGENERATION:
Virus infected neurons undergo degeneration.
Earliest change degeneration of Nissle's body- aggregated ribosomes in cytoplasm of neuron.
CLINICAL MANIFESTATION:
Inapparent infection 91-96% of cases Asymptomatic
Absorptive infection 5% Minor symptoms: fever,

malaise, anorexia, sore
throat, myalgia, headache
Non paralytic poliomyelitis 1% Aseptic meningitis
Paralytic poliomyelitis < 1% Descending asymmetric

acute flaccid paralysis
● Proximal muscles are affected earlier than distal muscles

● Paralysis starts at hip forwarded towards extremities
WILD POLIO VIRUS (WPV):

⮚ Strains: Wild poliovirus type 1 (WPV1), Wild poliovirus type 2 (WPV2), Wild
poliovirus type 3 (WPV3)
⮚ Strains are identical, produce similar manifestations, distinct genetically and
immunologically
⮚ WPV2 + WPV3 were eradicated in 1999 & 2019 respectively. Currently all cases are
caused by WPV1
VACCINE DERIVED POLIOVIRUSES (VDPVS):

● Produce poliomyelitis
● Clinically indistinguishable
● 3 types:
▪ circulating VDPVs (cVDPVs)
▪ immunodeficiency associated VDPVs (iVDPVs)
▪ ambiguous VDPVs (aVDPVs)
cVDPVs:
▪ Circulate in community
▪ Spread person to person by Feco oral transmission
▪ Occurrence is more common
PATHOGENESIS:
1. Transmission:
▪ Feco oral route
▪ Respiratory droplets (via inhalation)
▪ Conjunctival contact
2. Multiply locally in intestinal epithelial cells, submucosal lymphoid tissue,tonsil,Peyer
patches
● Hematogenous spread:
1. Regional lymph nodes
2. Spill into blood stream (primary viremia)
3. Further multiplication in reticuloendothelial system
4. Again enter blood stream (secondary viremia)
5. Spinal cord & Brain
● Neural spread:
1. Following tonsillectomy
2. Spread via glossopharyngeal nerve
1. Viral isolation-
● Specimen: Throat swab (upto 3 weeks of illness), Rectal swab (upto 12 weeks)
Viral isolation from CSF (blood is very rare)
● Transportation: Kept in frozen state

● Cell line: Primary monkey kidney cell – most recommended cell line
● Cell growth is identified by:
▪ Cytopathogenic effects
▪ Antigen detection
▪ PCR (targets VPI region of poliovirus)
2. Antibody detection :
● A rise in antibody titre in paired Sera collected at 1-2 weeks interval - suggestive of
poliomyelitis
● Most recommended method: Neutralisation test
● Only 1st infection with poliovirus produces strictly type specific responses
● Subsequent infections induce antibodies against group specific antigen common to all three
serotypes.
PROPHYLAXIS
Vaccine
Both inactivated and live polio virus vaccines are available
● Injectable polio vaccine

● Oral polio vaccine
▪ Injectable polio vaccine (Salk) - Virus is grown in monkey kidney cell line
1.5 ml of vaccine contains
● 40 units of type 1
▪ Oral polio vaccine (Sabin)
1.5 ml of vaccine contains
● 3 lakhs of type 1 virus
● 1 lakhs of type 2 virus
● 3 lakhs units of type 3 virus
RHINOVIRUSES:
● Respiratory route
● Cause Common cold
● >100 antigenic types
VIRUSES CAUSING ASEPTIC MENINGITIS:

● Group A and B Coxsackieviruses – Most commonly by A7 and A9 serotypes
● They are one of the type of Enterovirus
● They are classified into group A and B
● And each group is further classified as different serotypes
● Specimen collected – Stools, Swabs, CSF
● Isolation of virus – Suckling mouse intracerebral inoculation
● PCR vp1 gene is amplified
ESSAY 8
DESCRIBE THE MORPHOLOGY OF HIV, DESCRIBE THE PATHOGENESIS AND
LAB DIAGNOSIS OF HIV INFECTION. ADD A NOTE ON PRE EXPOSURE
PROPHYLAXIS
SHORT NOTE: LABORATORY DIAGNOSIS OF AIDS
HUMAN IMMUNODEFICIENCY VIRUS

- Belongs to Retroviridae family and genus Lentivirus
MORPHOLOGY:
▪ Spherical and 80-110 nm in size
▪ HIV is an enveloped virus
▪ ENVELOPE:
a) Lipid part – derived from the host cell membrane
b) Protein part – has 2 components:
1) Glycoprotein 120 (gp 120) – it is projected as knob like spikes on the
surface.
2) Glycoprotein 41 (gp41) – forms anchoring transmembrane pedicles
▪ NUCLEOCAPSID:
1. Capsid is isohedral in symmetry
2. Made of core protein.
3. Has a dense cylindrical inner core which has
- 2 identical copies of single stranded positive sense linear RNA
- Viral enzymes such as reverse transcriptase, integrate, proteases

HIV genes:
▪ Three structural genes – gag, pol, env

▪ Six non structural or regulatory genes
PATHOGENESIS:
Mode of transmission:
a) Sexual mode – most common method, accounts for 75% of total cases
b) Blood transfusion is the least common mode of transmission (5%) and risk of
transmission is maximum (90-95%)
Receptor attachment:
• CD 4 receptor on host cell surface is the main receptor and binds to gp 120
• Chemokine receptors act as second co- receptors and bind to gp120.
Ex: CXCR4 present on T lymphocytes.
CCR5 on cells of macrophage lineage.
• DC-SIGN facilitates transport of HIV by dendritic cells to lymphoid
organs.
REPLICATION:
1. After attachment of receptor to gp120, fusion of HIV to host cell by fusion protein gp 41
2. Nucleocapsid enter into host cell cytoplasm
3. Uncoating and release of 2 copies of ssRNA ,viral enzymes
4. Reverse transcriptase transcribes ssRNA to ssDNA
5. Endonuclease degrades ssRNA and ssDNA replicates to form dsDNA
6. The viral dsDNA gets integrated into host cell chromosome and forms pro virus with help
of integrase enzyme
7. HIV exhibits a latency period and it is able to replicate even in that state
DISEASE PROGRESSION:
Progressors Develops into AIDS % of PLHA
Typical progressor Within 10 years 80-90%
Rapid progressor Within 2-3 years 5-10%
Long term Non- progressor After long time (10-30 years) without A 5%
shows < 5000 HIV RNA copies /ml
Elite controller After long time (10-30 years) without A < 1%
shows < 50 RNA copies /ml
SCREENING TESTS (Detection of antibody):
1. ELISA (Enzyme Linked ImmunoSorbent Assay ):
▪ Most commonly performed screening tests. Easy to perform, sensitive, specific,

cost effective
▪ Types of ELISA-
● Indirect ELISA
● Competitive ELISA
● Sandwich ELISA
▪ Types of ELISA kits:
▪ Third generation ELISA uses recombinant and synthetic peptides as
antigen to detect HIV antibodies
▪ Fourth generation ELISA detects both HIV antibodies and p24 antigen
2. RAPID /SIMPLE TESTS:
● Works on various principles like: Immunochromatography, Dipstick / Comb
tests, particle agglutination assays
● Requires less than 30minutes to perform and does not require special
equipment.
SUPPLEMENTARY TESTS:
WESTERN BLOT ASSAY:
▪ Detects individual antibodies in serum separately against various antigenic fragments.

▪ Works on the principle of immunoblotting technique.
▪ Antigen antibody complexes appear as distinct bands on nitrocellulose strips.
CONFIRMATORY TESTS:
DETECTION OF p24 CORE ANTIGEN:
▪ P24 antigen is detectable after 12-26 days of infection, lasts for 3-6 weeks
▪ Detected by 4th generation ELISA
▪ Less sensitive as antibody formed binds to p24 antigen and the antigen antibody complex is
eliminated from blood
VIRAL RNA DETECTION :
▪ GOLD STANDARD method for confirmatory diagnosis

▪ Most sensitive, specific method
▪ Best tool for diagnosis of HIV during window period
DNA PCR:
▪ Extremely useful for diagnosis of pediatric HIV

▪ Differentiates latent HIV infection from active viral transcription
NON SPECIFIC IMMUNOLOGICAL TESTS:
CD4 CELL COUNT:
▪ By flow cytometry method

▪ Useful for assessing the risk of infections and monitoring the response to antiretroviral
therapy
POST EXPOSURE PROPHYLAXIS:

▪ Required to reduce the risk of transmission after occupational exposure
▪ Duration: Started within 2h of exposure and to be continued for 28 days

▪ Indication: If source is unknown / positive for HIV
▪ TL+LR Regimen: consists of Tenofovir – Lamivudine plus Lopinavir – Ritonavir
ESSAY 9
DISCUSS BRIEFLY ON IMMUNOPROPHYLAXIS OF VIRAL DISEASES. DISCUSS
BRIEFLY ON VIRAL VACCINES.
SHORT NOTES:
i. ORAL / SABIN POLIO VACCINE
ii. RABIES VACCINE
IMMUNOPROPHYLAXIS OF VIRAL DISEASE
ACTIVE IMMUNIZATION PASSIVE IMMUNIZATION
● (Pre-exposure prophylaxis) (Post-exposure prophylaxis)

● VIRAL VACCINES IMMUNOGLOBULINS
IMMUNOGLOBULINS:
● Used when an individual is immunodeficient
● No memory cells involved
● No role in prevention of subsequent infections
● Human Igs are used nowadays
● Ex: Human Igs are available for Mumps, Measles, Rabies
COMBINED IMMUNIZATION
Simultaneous administration of vaccines and immunoglobulins in post exposure prophylaxis is
extremely useful.
Ex: Rabies
LIVE ATTENUATED VACCINES

● Preparation: Attenuated by serial passages (except: smallpox)
● Advantages: Gives strong and long-lasting immunity, single dose is sufficient (except:
OPV)
● Disadvantages: Less stable, Risk in immunodeficient and pregnant people.
Ex: MUMPS, MEASLES, RUBELLA, CHICKEN POX, SMALLPOX
KILLED VACCINES
● Preparation: Inactivating viruses with formalin, phenol and not with UV since it has a
risk of multiplicity reactivation
● Advantages: Stable, safe for immunodeficient and pregnant people
● Disadvantage: Adverse side effects due to reactogenicity which can be reduced by
purification of viruses.
Ex: Rabies (Neural and Non-neural)
SUBUNIT VACCINE
● Preparation: rDNA technology
● Advantage: No side effects
● Disadvantage: Costly
ORAL POLIO VACCINE/ SABIN VACCINE (SHORT NOTE):

▪ Live attenuated vaccine
▪ Formulation: Trivalent (1,2,3 serotypes)
o Bivalent (1,3 serotypes)
o Monovalent (any one serotype)
▪ National immunization schedule: 5 DOSES (2 dose of Bivalent)
o zero dose – birth
o 1,2,3 – 6th 10th 14th week
o Booster – 1 – 24 months
▪ Efficacy: 90 – 100% (1/2 doses of OPV)
ADVANTAGES:
● HERD IMMUNITY:
OPV shorts sheds in feces
Spread in community
Induce herd immunity
● LOCAL IMMUNITY
OPV induces mucosal IgA production
● Cheap
DISADVANTAGES:
● Unstable – Require stringent conditions
Storage at – 20 degree Celsius, Stabled in MgCl2,
Maintained in pH less than 7
● Risk to give to immunodeficient and pregnant peoples

● Efficacy decreases when breastfeeding, diarrhea, interference by enterovirus
● OPV can cause VAPP and VDPV
VAPP-Vaccine Associated Paralytic Poliomyelitis
VDPV- Vaccine derived Polio virus
RABIES VACCINE (SHORT NOTE)

Reference: Essentials of Medical Microbiology, Apurba Sastry E/3: Page No. 722
TYPES:
● Purified Chick Embryo Cell (PCEC)
● Purified Vero Cell (PVC)
● Human Diploid Cell (HDC)
ROUTES: Intradermal or Intramuscular
SITE: Deltoid for adults, Anterolateral area of thigh for children (age below 2)
DOSE: One ID dose- 0.5 ml, One IM dose – entire vial

SCHEDULE OF PEP REGIMEN: (PEP- Pre exposure prophylaxis)
ID regimens are cost effective, dose sparing, time sparing. So ID is preferred over IM
ID PEP regimen (2-2-2): 2-site on 0,3,7 days
IM PEP regimen (4 doses)
1. Site on 0,3,7 and 4th dose between 14 to 28 days

2. Site on day 0 and 1 – site IM on days 7 and 21
INTERCHANGE:
Changes in vaccine product routes (IM or ID) during the same PEP course are acceptable if
unavoidable.
IF DELAYED:
If vaccine dose is delayed for any reason PEP regimen should be resumed.
PEP FOR INDIVIDUALS PREVIOUSLY VACCINATED:

● RIG is not necessary regardless of exposure category.
● They need local wound care and an accelerated vaccine regimen consisting of any
of the following schedules
▪ Site ID vaccine given on days 0 and 3 or
▪ Site IM vaccine given on days 0 and 3 or
▪ Site ID vaccine given on day 0 only (left and right deltoids, thigh)
NOTE: If repeat exposure occurs within 3 months of receiving PEP only local wound treatment
is required.
PEP IS RECOMMENDED IN TWO CONDITIONS:

● For individuals at higher occupational risk
● For subpopulation in remote endemic areas
PEP REGIMEN (FOR ALL AGES):

Schedule:
▪ Site ID vaccine given on days 0 and 7

▪ Site IM vaccine given on days 0 and 7
Booster:
No need to take PEP booster periodically only if continued high risk of rabies exposure remains
a routine PEP booster is recommended.
Following Exposures:
● An accelerated vaccine regimen is indicated

● Rabies Immunoglobulin (RIG) is not necessary.
ESSAY 10
DISCUSS VARIOUS METHODS FOR ISOLATION OF VIRUSES IN THE
LABORATORY.
SHORT NOTES:
i. TISSUE CULTURE FOR VIRUSES
ii. VIRAL INCLUSION BODIES
iii. CYTOPATHIC EFFECTS
iv. VIRAL CELL CULTURE
v. EGG CULTURE
LABORATORY ISOLATION OF VIRUSES :
- Viruses cannot be grown on artificial culture due to

▪ Lack of individual metabolic machinery
▪ Total dependence on host for replication
- Specimens collected should be transported immediately to the laboratory along with
refrigeration in liquid N2 at -196℃, as most viruses are heat labile.
ANIMAL INOCULATION:
- Due to ethical issues surrounding the use of animals in scientific study, animal
inoculation is restricted to the study of viral pathogenesis and viral vaccination trails.
Egg culture:
Embryonated hen’s egg is used for inoculation.
Sites for inoculation in embryonated egg:
1. Yolk sac: Arbovirus inoculation

2. Amniotic sac: Isolation of influenza virus
3. Allantoic sac: As it is a larger sac, it is used for better yield of viral vaccines for influenza
virus and yellow fever
4. Chorioallantoic Membrane: Isolation of poxvirus
This method was largely used in the past but is limited in present times.
Tissue culture:
Poliovirus – first cultivated through tissue culture
Three types:
1. Organ culture: Used for certain viruses which have affinity towards specific organs.
Ex: Tracheal ring culture for coronavirus
2. Explant culture: Minced tissue is grown as explants

3. Cell line culture: Cell lines are prepared and used for isolation.
Preparation of cell lines:
Tissue
Individual cells
Suspend the cells in viral growth medium containing vitamins, minerals, growth supplements,
pH buffer, phenol red as pH indicator
Viral growth medium is suspended in tissue culture flask
Monolayer is formed on glass surface after incubation

TYPES OF CELL LINES:
1. Primary cell lines:
● Normal tissue
● Freshly taken from organs
● Limited divisions of up to 5-10 times
● Diploid karyotype
● Used for primary isolation and vaccine production
● Ex: Human amnion cell line
2. Secondary cell lines
● Taken from normal tissue
● 10-50 divisions
● Diploid karyotype
● Ex- Human fibroblast cell line
3. Continuous cell lines:
● Derived from cancer cells
● Capable of indefinite divisions
● Altered haploid karyotype
● Ex- HeLa cell line
DETECTION OF VIRAL GROWTH IN CULTURE
CYTOPATHIC EFFECT:
- Morphological changes produced by a host cell shown by a virus in a cell line as seen
through a light microscope is called cytopathic effect.
▪ CPE occurs when an infected cell is lysed by a reproducing virus.
▪ Morphological changes:
1. Rounding of cell
2. Syncytia formation
3. Appearance of cytoplasmic inclusion bodies
▪ Not all viruses produce CPE
▪ Type of CPE is different for different viruses, and is used for their identification
Shell vial technique:
▪ Used for viruses taking long time to show CPE

▪ Method:
Sample centrifugation
Enhancing cell contact and viral replication
Detection of viral antigen in host cell by direct fluorescence method
Other methods:
1. Detection of viral genes by PCR

2. Electron microscopy
ESSAY 11
DESCRIBE THE MORPHOLOGY, PATHOGENESIS AND LAB DIAGNOSIS

INFLUENZA VIRUS.
SHORT NOTES:
i. DIAGNOSIS AND PROPHYLAXIS OF H1N1 INFECTION.
ii. RECENT SWINE FLU PANDEMIC.
iii. PROPHYLAXIS OF INFLUENZA.
iv. INFLUENZA VIRUSES.
INFLUENZA VIRUS
Family – Orthomyxoviridae
Four genera – Influenza A, B, C, D
MORPHOLOGY
● Shape- spherical
● Size- 80-120 nm
● Enveloped virus with two peplomers – Haemagglutinin and neuraminidase
● Helical nucleocapsid
● Negative single stranded segmented RNA genome (Influenza A &B - 8 segments of RNA
and Influenza C&D - 7 segments of RNA)
● Replication occurs in nucleus (* only RNA virus replicate in nucleus)
● Viral proteins- 8 structural {PB1, PB2, PA, NP, HA, NA, M1, M2} and 2 non-structural
proteins {NS1, NS2}
Reference: Essentials of Medical Microbiology, Apurba Sastry E/3: Page No. 648 Fig. 66.1
Gene Gene product Function

segment
1 PB1 Polymerase
2 PB2 Polymerase
3 PA Polymerase
4 HA Haemagglutinin – binds to receptor on RBC forms

hemagglutination
5 NP Nucleocapsid protein, encloses genome
6 NA Neuraminidase – replaces HA from RBC and cause

elution (reversal of hemagglutination)
7 M1 Matrix protein – forms shell underneath envelope

M2 Ion channels – transport molecules across envelope
8 NS1 Interferon antagonist, inhibits pre-mRNA splicing

NS2 Transport of molecules across nucleus
TYPES OF INFLUENZA VIRUS

Based on ribonucleoprotein (RNP) and matrix protein (M protein) influenza viruses
is divided into 4 genera: A, B, C and D
INFLUENZA A VIRUSES
● Genome segments - 8
● Host range – animals, birds & humans
● Epidemiology – epidemic & pandemic
● Subtypes – based on HA & NA .... HA subtypes: 18 & NA subtypes: 11
● Human subtypes: 6 HA (H1, H2, H3, HT, H7 & H9) & 2 NA (N1 & N2)
INFLUENZA B VIRUSES
● Genome segments – 8
● Host range – humans
● Subtypes – no subtypes
● But diverged into lineages
● Either belong to either B/Yamagata or B/Victoria lineage
INFLUENZA C VIRUSES
● Host range – man, pigs
● Less frequently detected, cause mild infections
INFLUENZA D VIRUSES
● Host range – animals
● Not pathogenic to humans
PATHOGENESIS
Inhalation of respiratory droplets, via contact with contaminated surfaces or fomites
HA attaches to specific sialic acid receptors on respiratory mucosa
Virus enters the cell
Virus replicate in the infected cells
Infectious daughter virions spread to adjacent respiratory epithelial cells

Virus spread to lower respiratory tract or spills over bloodstream
Cause cellular destruction and desquamation of mucosa of respiratory tract
Predisposes to secondary bacterial infection
RECENT SWINE FLU PANDEMIC:

● Virus – Influenza A (H1N1)
● Emerged in California
EPIDEMIOLOGY:
● Origin: Genetic reassortment of 4 strains – 1 human strain + 2 swine strains + 1 avian
strain – mixing occurred in pigs
● Transmission: Human to human
● Less virulent (as it lacks PB1 F2 protein) so, it has caused more morbidity but less
mortality
CLINICAL FEATURES:
● Uncomplicated influenza: Mild upper respiratory tract illness and diarrhoea
● Complicated influenza: Secondary bacterial pneumonia, dehydration, CNS involvement
and multiorgan failure.
CATEGORISATION OF SEASONAL INFLUENZA A/H1N1:
Category Definition Laboratory testing, treatment, isolation
Category A Influenza like illness (ILI) Laboratory tests - not required
Mild fever, cough/sore throat, headache Treatment - only symptomatic, antiviral

diarrhoea and vomiting drugs not required
Isolation- confine at home, avoid contact

with public and family members
Category B Category A plus any one: Laboratory tests- not required
a) High- grade fever, sore throat Treatment - symptomatic requires

treatment, antiviral drug require(
b) Presence of risk factors like Diabetes oseltamivir or Zanamivir)
mellitus, obesity, AIDS, chronic pulmonary,
cardiac and renal disorders Isolation- confine at home, avoid contact
with public and family members
Category C Severe acute respiratory syndrome (SARI) Laboratory tests- required
Category B plus any one Immediate hospitalization- required
a) breathlessness, chest pain, fall in BP, sputum Treatment - start antiviral drugs
+ blood, bluish discoloration of nails immediately without delay
b) children having ILI manifest with red flag Isolation - droplet precaution to be
signs - inability to feed well, difficulty in followed
breathing
c) worsening of underlying chronic causes
LABORATORY DIAGNOSIS
1. SPECIMEN COLLECTION:
▪ Nasopharyngeal swab, lavage fluid, nasal aspirate
▪ Transport – swab is kept inside viral transport media at 4°C
2. ISOLATION OF VIRUS:
▪ Inoculation in embryonated eggs and primary monkey kidney cell lines

▪ Growth is detected by hemadsorption, haemagglutination test
▪ As it is difficult to isolate, it is not routinely used
3. DIRECT IMMUNOFLUORESCENCE TEST:
▪ Viral antigens coated on epithelial cells can be detected in nasal aspirates by

using fluorescent tagged antibodies
▪ Rapid but less sensitive
4. MOLECULAR METHODS:
A) RT-PCR:
▪ More sensitive, specific and rapid

▪ Turnaround time < 1day
▪ Also detect specific type and subtype of influenza virus
B) Real - time RT-PCR:
▪ Gold standard method – quantitative, highly sensitivity and specificity

than RT-PCR
▪ Turnaround time 2-3 hours
▪ Simultaneously detect three common seasonal flu strains - A/H1N1,
A/H3N2 and type B
Real-time RT-PCR for seasonal influenza types

C) Bio Fire Film Array Respiratory Panel (RP):
▪ Detect 20 respiratory pathogens simultaneously like Influenza A, Influenza A/H1,

Influenza A/H3, Influenza A/H1-2009 and Influenza B
5. ANTIBODY DETECTION (SEROLOGY):
▪ Detect subtype specific serum antibodies using specific antigens

▪ Useful for sero – epidemiology purpose, not for clinical diagnosis
▪ Available tests – ELISA, neutralization test and haemagglutination inhibition test
(HAI)
TREATMENT:
● Specific antiviral therapy
● Start within 48hrs of onset of symptoms
● Neuraminidase inhibitors
▪ Administered for influenza A and Influenza B infections
▪ Drug of choice for A/H1N1 2009 flu, A/H5N1 avian flu and Influenza B
▪ Dosage –
✔ Oseltamivir (Tamiflu 75mg tablets)
✔ Zanamivir (10mg, inhalation form)
▪ Schedule – For treatment – given twice a day for 5 days
▪ For chemoprophylaxis – given once daily
Duration depends on clinical setting; usually 7 days
● Matrix protein M2 inhibitor
▪ Amantadine and rimantadine - given for influenza A virus infection
▪ Other strains like A/H1N1 2009 FLU and A/H5N1 avian flu and Influenza B
virus had developed resistance
ESSAY 12
DISCUSS THE PATHOGENESIS, CLINICAL FEATURES, COMPLICATIONS,
LABORATORY DIAGNOSIS OF RUBELLA VIRUS. ADD A NOTE ON ITS
PREVENTION.
SHORT NOTE: MMR VACCINE
RUBELLA VIRUS (GERMAN MEASLES)

● Mild exanthematous fever
● With Transient fever, lymphadenopathy
● Pregnant women – causes congenital malformations
● Trivial (MMR)
PROPERTIES:
● Pleomorphic, spherical
● 50-70 nm in diameter
● Single stranded RNA genome
● Surrounded by hemagglutinin peplomers
● Resembles Toga virus
● Family: Togaviridae
● Genus: Rubivirus
● Accumulates human RBC at 4°C
CLINICAL FEATURES:
● Infection by Inhalation
● Incubation period: 2-3 weeks
● Rash on face, neck, trunk, palms and soles
● Mainly in children
COMPLICATIONS:
● Arthralgia, arthritis
● Common in women
● Causes chromosomal breakages, inhibition of mitoses
● Virus in throat disappear in 7 days
● Viremia at 7th day before rash
● Infection to fetus by maternal blood
CONGENITAL RUBELLA:
Fetal damage by stage of pregnancy
1. Very early pregnancy: Ends in abortion

2. First trimester: 90% of congenital
3. Later on in pregnancy: Developmental retardation in child
CONGENITAL RUBELLA SYNDROME:

● Causes are cardiac defects, cataract, deafness
● Expanded Rubella Syndrome:
Hepatosplenomegaly
Thrombocytopenic purpura
Myocarditis
Bone lesions
● Present in all excretions

● Present in tissues as cataractous lenses for several years
● No routine diagnosis needed
● Diagnosis important in suspected pregnancy
DIAGNOSIS IN PREGNANCY:
1. SEROLOGY:
▪ Mainstay of diagnosis
▪ ELISA – to detect IgM, IgG
▪ IgM without IgG – Current acute Infection
▪ IgG without IgM – Past infection / vaccination / Infection
▪ Screening Test – TORCH Panel (In pregnant women)
2. CULTIVATION:
▪ Grown in 1° cell cultures, continuous cell lines
▪ Virus isolation is not commonly used for diagnosis due to delay
▪ Isolated from blood, throat swabs in rabbit
▪ Virus grows better in 33 – 35 ° C
DIAGNOSIS OF CONGENITAL RUBELLA:

1. SEROLOGY:
▪ IgM in newborn indicates intrauterine infection
▪ IgM not crosses placenta indicates response of fetus to infection
▪ IgG present in newborn after 6 months in congenital infection
2. ISOLATION:
▪ From urine, throat swabs, leucocytes bone marrow, CSF
PROPHYLAXIS:
● Confers lasting immunity as it has 1 antigenic type
● Live attenuated infection developed in tissue culture
● RA 27/3 strain is the vaccine used today
● Given by subcutaneous injection alone / combination with MMR vaccine
● Lymphadenopathy, rash, arthralgia may occur sometimes
● Not prescribed for immunodeficient patients
● Pregnancy should be avoided for 3 months after vaccination
● Not teratogenic
EPIDEMIOLOGY:
▪ Worldwide in distribution
▪ 80 – 90 % are immune by 15 years
▪ 10 – 20 % of mothers are non-immune, vulnerable
ESSAY 13
DISCUSS THE PATHOGENESIS, CLINICAL FEATURES, COMPLICATIONS,
LABORATORY DIAGNOSIS OF MEASLES VIRUS. ADD A NOTE ON ITS
PREVENTION.
SHORT NOTES:
1. MMR VACCINE
2. WARTHIN FINKELDEY GIANT CELLS
3. MEASLES VIRUS
MEASLES
- Childhood disease (highly contagious)

- Characterized by – fever and respiratory symptoms, followed by typical maculopapular
rash
PATHOGENESIS:
● Transmission: Occurs predominantly via the respiratory route either by Droplet inhalation
or Small-aerosol particles
● Spread: The virus multiplies locally in the respiratory tract; then spreads to the regional
lymph nodes --- enters into the bloodstream and infect monocytes (primary viremia)
----further multiplies in reticuloendothelial system ---- spills over into blood (secondary
viremia) --- disseminates to various sites.
● Target sites: The virus is predominantly seeded in the epithelial surfaces of the body,
including the skin, respiratory tract, and conjunctiva.
- Incubation period is about 10 days which may be shorter in infants and longer (up 3
weeks) in adults. Disease can be divided into three stages.
i) Prodromal Stage:
▪ This stage lasts for 4 days (i.e., from 10th to 14th day of Infection) and is characterized
by manifestations such as
- Fever occurs on day 1 (i.e., on 10th day of infection).
- Koplik's spots are pathognomonic of measles, appear after two days following fever
(i.e., on 12th day of infection) and are characterized by White to bluish spot (1mm size)
surrounded by an erythema. Appear first on buccal mucosa near second lower molars.
Rapidly spread to involve the entire buccal mucosa and then fade with the onset of rash.
- Non-specific symptoms may be present such as cough, nasal discharge, and redness of
eye, diarrhea or vomiting.
ii) Eruptive Stage:
▪ Maculopapular dusky red rashes appear after 4 days of fever (i.e., on 14th day of
infection).
- Rashes typically appear first behind the ears -- then
- Spread to face, arm, trunk and legs -- then fade in the same order after 4 days of onset.
- Rashes are typically absent in HIV infected people.
Fever (10th day) - > Koplik's spot (12th day) - >rash (14th day)
iii) Post Measles Stage:

- It is characterized by weight loss and weakness. There may be failure to recover and
gradual deterioration into chronic illness.
COMPLICATIONS:
1. Secondary Bacterial Infections:
▪ Following measles, there is profound immune suppression and fall of cell mediated
immunity which in turn predisposes to various secondary bacterial infections.
▪ Otitis media and bronchopneumonia are most common.
▪ Recurrence of fever or failure of fever to subside with the rash.
▪ Worsening of underlying tuberculosis with a false positive Mantoux test.
2. Complications Due to Measles Virus Itself:
▪ Giant-cell pneumonitis (Hecht's pneumonia) in immunocompromised children,

and HIV infected people.
▪ Acute laryngotracheobronchitis (croup)
▪ Diarrhea leads to malnutrition including vitamin A deficiency.
3. Central Nervous System Complications:
- CNS complications are rare, but most severe.
▪ Post-measles encephalomyelitis: It develops within 2 weeks of onset of rash. It represents
an autoimmune response against the myelin basic protein.
▪ Measles inclusion body encephalitis occurs months after rashes.
▪ Subacute sclerosing pan encephalitis (SSPE): It is a slowly progressive disease
characterized by seizures and progressive deterioration of cognitive and motor functions.
SSPE belongs to group C slow virus infection, caused by a defective measles virus.
▪ Age: SSPE typically develops if the primary measles virus infection occurs in children
less than 2 years of age. SSPE usually develops after 7- 13 years after primary measles
infection. It is fatal within 1- 3 years of onset. High titre antibody to measles virus in CSF
is diagnostic.
1. SPECIMEN: Nasopharyngeal swab
2. ANTIGEN DETECTION: By using anti-nucleoprotein antibodies in virus infected cells.
3. VIRUS ISOLATION: Monkey or human kidney cells / Vero cell line produces cytopathic
effect as multinucleated giant cells (Warthin Finkeldey cells).
Reference: Essentials of Medical Microbiology, Apurba Sastry E/2: Page No. 486 Fig. 44.7 C
WARTHIN FINKELDEY CELLS:
- They are the multinucleated giant cells containing both intranuclear and intracytoplasmic
antibodies. It is a cytopathic effect observed after 7 to 10 days of inoculation into cell
lines.
- Shell vial culture is recommended for early detection in 2- 3 days.
4. ANTIBODY DETECTION:
▪ Detection of measles-specific IgM antibody in serum or oral fluid or four-fold rise of IgG
antibody titre between acute and convalescent-phase sera is taken as significant.
▪ Demonstration of high titer measles antibody in the CSF is diagnostic of SSPE.
▪ ELISA is the most recommended test that uses recombinant measles nucleoprotein (NP)
antigen.
5. REVERSE TRANSCRIPTASE PCR (RT-PCR): Specific for measles RNA detection is

available.
▪ It is extremely sensitive and specific; it may also permit characterization of measles virus
genotypes for molecular epidemiologic studies.
▪ It can distinguish wild-type from vaccine virus strains.
▪ RNA can be detected in specimens up to 10- 14 days post rashes, in contrast to virus
isolation, which often becomes negative after 3 days of rash.
PREVENTION:
- By live Attenuated Measles Vaccine
▪ Strains: Most attenuated strains in use currently are derived from the original Edmonston
strain.
▪ Vaccine is prepared in the chick embryo cell line.
▪ Reconstitution: Vaccine is available in lyophilized form and it has to be reconstituted with
distilled water and then should be used within 4 hours.
▪ Vaccine is thermo labile, hence it must be stored at - 20°C.
▪ One dose (0.5 mL) containing more than 1000 infective viral units is administered
subcutaneously.
▪ Indication: Under the national immunization schedule of India, measles vaccine is given at 9
months (because maternal antibody disappears by this time) along with vitamin-A
supplements.
▪ However, it can be given at 6 months during a measles outbreak, in that case a second dose
should be given at 9 months.
▪ Combined vaccines: Measles vaccine is available in combined form with mumps and
rubella vaccine (MMR vaccine) and with varicella (MMR-V vaccine).
▪ Side effects: Mild measles like illness may develop in 15-20% of vaccines. There is no
spread of the vaccine virus in the community. Toxic shock syndrome (due to contamination
of vial with Staphylococcus aureus toxins).
▪ Contacts: Susceptible contacts over 9-12 months may be protected against measles if the
measles vaccine is given within 3 days of exposure. This is because the incubation period of
measles induced by the vaccine strain is about 7 days, compared to 10 days for the naturally
occurring measles. Measles immunoglobulin (Ig) can also be given within 3 days, at a WHO
recommended dose of 0.25 mg/ kg of bodyweight. However, both vaccines and Ig should not
be given together. At least 8- 12 weeks of gap must be maintained.
ESSAY 14
CLASSIFY CORONAVIRUSES. DISCUSS THE MORPHOLOGY, PATHOGENESIS,
CLINICAL FEATURES, LABORATORY DIAGNOSIS, TREATMENT & PREVENTION
OF COVID-19. EXPLAIN IN DETAIL THE RECENT COVID-19 PANDEMIC AND
OTHER PREVIOUS OUTBREAKS.
COVID – 19
CLASSIFICATION OF CORONAVIRUS:
Family: Coronaviridae
Subfamily: Coronavirinae and Torovirinae
Genera:
Coronaviridae:
● Alphacoronavirus
● Beta coronavirus
● Gamma coronavirus
● Delta coronavirus
Alphacoronavirus:
● Human coronavirus 229E

● Human coronavirus NL63
Beta coronavirus:
● Human coronavirus HKU1

● Human coronavirus OC43
● SARS – CoV
● Mers – CoV
● SARS-CoV-2 (COVID – 19)
MORPHOLOGY:
● Enveloped, petal shaped peplomers

● Pleomorphic
● Helical symmetry
● Unsegmented +ve sense RNA genome
● Consists of 4 structural and16 non structural proteins
● Structural proteins
- Nucleocapsid – Consists of positive sense single stranded RNA
- Spike protein – Helps in attachment
It consists of two subunits:
▪ S1 subunit- posses receptor binding domain binds to ACE2 receptor

▪ S2 subunit-facilitates viral cell membrane fusion
- Membrane glycoprotein- gives shape to virus
- Envelope protein- transmembrane protein with ion channel activity
● Non-structural proteins – help in replication of virus

Ex: RNA dependent RNA polymerase
Helicase
PATHOGENESIS:
● Mode of transmission – droplet transmission, airborne transmission
● Incubation period – 5 to 6 days as long as 14 days
● Colonize in upper respiratory tract and reach the alveoli
VIRAL ENTRY:
Reference: Essentials of Medical Microbiology, Apurba Sastry E/3
VIRAL REPLICATION:
HOST RESPONSE:
● Damage to pneumocytes – release of cytokines – activate pulmonary macrophages –
release IL-1, IL-6, TNF
● These cytokines – cause contraction of endothelial cells and increase vascular
permeability – accumulation of fluid in the alveoli
● Compression of alveoli – decrease surfactant – collapse of alveoli
● Neutrophils also migrate across the vascular wall and release protease and reactive
oxygen species
● They cause injury to damage to nearby type1 pneumocyte – cause difficult to exchange –
hypoxemia
● Alveolar macrophage activates T cell – release interferons and also CD8 T cell kill the
virus infected cells
● In later stage – recruitment of fibroblasts causes lung fibrosis – respiratory failure
Reference: Essentials of Medical Microbiology, Apurba Sastry E/3
- Hypoxemia stimulate sympathetic system – Increased heart rate and increase respiratory
rate
- As inflammatory response increases, it increases capillary permeability in other organs
- It decreases blood volume that leads to hypotension and result in decreased organ
perfusion
- As a result – multiple organ failure
CLINICAL FEATURES:
● Breathlessness
● Cough with expectoration
● Fever
● Sore throat
● Headache
● Loss of taste or smell
● Repeated shaking with chills
● Muscle or body aches
● Sample collection – nasopharyngeal swab, oropharyngeal swab
● Swab used – dacron / rayon / polyester swab
● Transport medium – viral transport medium
1. NUCLEIC ACID AMPLIFICATION TEST -RT PCR

▪ Viral RNA is converted into complementary DNA using reverse transcriptase
enzyme
Reference: Essentials of Medical Microbiology, Apurba Sastry E/2: Page No. 65
▪ Gold standard test for diagnosis of COVID – 19

▪ Average time taken – 4 to 5 hours
▪ Gene targets –
- For screening – spike protein, envelope protein, membrane protein, nucleocapsid protein
- For confirmation – RNA dependent RNA polymerase, open reading frames (ORF1a/b)
● It is detected by quantitative PCR

Principle – Target gene is first amplified
● When the amplicon binds to probe the fluorescence is emitted

● No of virions inversely proportion of cycle time
● Sample is positive- cycle time greater than 40 cycles
2. ANTIGEN DETECTION TEST
▪ To detect nucleocapsid and spike protein antigen using immunochromatographic test

Procedure:
- Nasopharyngeal or oropharyngeal swab used – added to viral extraction buffer – mixed

and add 2 to 3 drops to a well of strip – wait for 15 minutes
- Positive – control and test band
- Negative – control band (if negative, confirm by RTPCR)
▪ ELISA and Chemi Immunofluorescence assay also used
3. ANTIBODY DETECTION TEST
● IgM: It appears at the end of first week and disappears in 3-4 weeks
● IgG: At the end of Second week
● Detected by immunochromatographic test
INTERPRETATION:
● IgM – Infection occurred in last one week

● IgG and IgM infection occurred in last 14 days
● IgG – Infection occurred in 3-4 weeks back
● Only control band – not an infection or early infection
● It is useful in:
- Sero surveillance purpose
- The survey in high risk (health workers, frontline workers)
4. PROGNOSTIC MARKERS
● Elevated lL-6 – Indicates cytokine storm

● Elevated d-dimer – Indicates fibrin degradation product underlying coagulopathy
● Elevated serum ferritin – Indicate inflammation
● Severe lymphopenia
● Elevated C – reactive protein – Indicates acute inflammation
5. CT SCAN – Ground glass appearance
TREATMENT:
Symptomatic management:
- Supplemental oxygen therapy given immediately

- High flow nasal cannula oxygenation
- Non invasive mechanical ventilation
- Investigational therapy
Drugs:
● Imedinivimab, Casirivimab – Inhibit binding to ace-2

● Favipiravir, Remedesivir – Drugs which inhibit RNA polymerase
● Lopinavir, Ritovir – protease inhibitors
● Tocilizumab – Inhibit IL- 6
● Drugs which reduce mortality
- Steroids - reduce cytokine production
- Anticoagulants- low molecular weight heparin and unfractionated heparin
CHEMOPROPHYLAXIS – Hydroxychloroquine
● Indication – all asymptomatic health care workers, asymptomatic frontline workers

● Contraindication – retinopathy, Hypersensitivity to HCQ, pre-existing cardiomyopathy,
pregnancy and lactation
● ECG to be done before prescribing and during the course to check for prolongation of
QT Interval
COVID -19 VACCINE:

▪ Covaxin – Inactivated vaccine contains spike protein
(2 doses 4 weeks apart- IM route)
▪ Covishield – Modified chimpanzee adenovirus expressing spike protein

(2 doses 4weeks apart- IM route)
PREVENTION:
For health care workers
● Hand hygiene
● Personal protective equipment
● Environmental cleaning
For general public:
● Hand wash
● Social distancing
● Environmental cleaning
● Wearing cloth mask
COVID- 19 PANDEMIC:
● SARS-CoV- 2 originated in Wuhan, China on Dec 2019
● On 30th Jan 2020, India reported the first case
● On 11th Feb 2020, new coronavirus called COVID 19
● On 11 March 2020, WHO officially declared COVID 19 as Pandemic
● Covid 19 spread started on 13 March 2020
● During the later phase there is emergence of new variants – UK variant, South African
variant
OTHER RECENT OUTBREAKS:
SARS-CoV – first pandemic of 21st century
● Originated in china on 2002- 2003

● From civet cat, raccoon dogs
● Clinical manifestations- sore throat, fever, muscle pain, headache
MERS- CoV
● Originated in Saudi Arabia- 2012

● From dromedary camels
● Clinical manifestation- fever, cough, shortness of breath
ESSAY 15
DEFINE & CLASSIFY SLOW VIRUS DISEASES. DISCUSS THE MECHANISM,
CLINICAL MANIFESTATIONS, LABORATORY DIAGNOSIS & TREATMENT OF
PRION DISEASES. HOW WILL YOU STERILIZE THE PRION CONTAMINATED
MATERIALS?
SHORT NOTE: SLOW VIRUSES / SLOW VIRAL DISEASE OF MAN
SLOW VIRUS DISEASES

- Group of infections in animals and human beings with –
1. Very long incubation periods ranging from months to years
2. Slow, relentless course of illness lasting for months or years, with remissions
and exacerbations
3. Predilection for involvement of the central nervous system
4. Absence of immune response or an immune response that does not arrest the
disease, but may actually contribute to pathogenesis
5. Genetic predisposition
6. Invariable fatal termination
CLASSIFICATION:
a) Group A: Caused by serologically related, non-oncogenic retroviruses called Lentiviruses
1. Sheep –Visna (demyelinating disease), Maedi (progressive pneumonia)

2. Humans – HIV (AIDS)
b) Group B: Prion diseases of the CNS
Collectively known as the subacute spongiform viral encephalopathies
1. Human disease: Kuru, Creutzfeldt-Jakob disease

2. Animal disease: Scrapie, Mink encephalopathy, Mad cow disease
c) Group C: 2 unrelated CNS diseases of human beings
1. Subacute sclerosing panencephalitis (SSPE)

2. Progressive multifocal leukoencephalopathy (PML)
GROUP B – PRION DISEASES

- Transmissible spongiform encephalopathies (subacute spongiform viral
encephalopathies)
- Chronic progressive degenerative diseases of the CNS
PRIONS:
i. Infectious agents
ii. Proteinaceous in nature
iii. Devoid of DNA and RNA
iv. Unusually resistant to physical and chemical agents such as heat, irradiation and
formalin
v. Can be transmitted to experimental animals by parenteral and oral challenge
MECHANISM OF PRION DISEASES:

1. Once infected, the prion proteins (PrPsc) are carried to the neurons
2. They bind to the normal PrPc on the cell surface
3. This causes release of PrPc from cell surface
4. Followed by post translational modification– elongated polypeptide PrPc becomes
globular polypeptide PrPsc
5. The cell synthesizes new PrPc and the cycle is repeated
6. As a result, large amount of PrPsc is formed
7. PrPsc are aggregated as amyloid-like plaques in the brain
8. As these plaques consist of host proteins, there is lack of an immune response or
inflammation
9. PrPsc are internalized by neurons and get accumulated inside the cytoplasmic vacuoles
giving the cell a spongiform appearance
10. PrPsc are transmissible – infectious, inheritable
PATHOLOGY:
Spongiform encephalopathy – main pathology seen in CNS:
1. Vacuolation of the neurons

2. Formation of amyloid-containing plaques and fibrils
3. Proliferation and hypertrophy of astrocytes
4. Fusion of neurons and adjacent glial cells
Incubation period – varies from months to years (longest being30 years). But once disease
sets in, progression is fast
1. Prodromal phase lasts for 3- 5 months, followed by appearance of manifestations such as

loss of muscle control, shivering, myoclonic jerks, tremors, loss of coordination and
rapidly progressive dementia
2. Death occurs within 1 year of onset of disease
HUMAN PRION DISEASES:
CREUTZFELDT-JAKOB DISEASE (CJD):
1. Classical form – most common (85% cases)

2. A subacute, presenile encephalopathy
3. Progressive incoordination and dementia
4. Ending fatally in about a year
Other Forms:
a) Sporadic CJD: Due to somatic mutation or spontaneous conversion of PrPc into

PrPsc
b) Iatrogenic CJD (50-75 yrs age): Transmitted by direct contact during some
medical or surgical procedures contaminated with prion tissues
i. Corneal transplantation
ii. Injection of the pituitary growth hormone
iii. Dura mater graft implantation
iv. EEG electrode implantation
c) Variant CJD (Below 30 yrs age): Believed to be transmitted through consumption
of contaminated beef with BSE prions
d) Familial CJD: Due to inheritance of mutation of the PrP gene
i. Gerstmann-Straussler-Scheinker (GSS) syndrome
ii. Fatal familial insomnia
KURU:
1. Was seen only in the Fore tribe inhabiting the eastern highlands of New Guinea.
2. The disease had an incubation period of 5-10 years
3. Progressive cerebellar ataxia and tremors
4. Ending fatally in 3-6 months
5. Believed to have been introduced through cannibalism and maintained by the tribal
custom of eating the dead bodies of relatives after death as a part of a ritual
6. The disease has disappeared following the abolition of cannibalism
ANIMAL PRION DISEASES:

1. Scrapie: Prototype prion disease, affects sheep
2. Mink encephalopathy: Scrapie-like disease of mink
3. Bovine spongiform encephalopathy (BSE): Mad cow disease
1. Measurement of PrPsc by conformation dependent immunoassay – most definitive
diagnostic tool for prion diseases
2. Neuropathological diagnosis in brain biopsies: The pathological hallmarks of prion
diseases seen under light microscopy, are spongiform degeneration and astrocytic gliosis
with lack of inflammatory response
3. Sequencing the PRNP gene to identify the mutation - important in familial forms of
prion diseases
4. Abnormal EEG: In late stage of the disease, high-voltage, triphasic sharp discharges are
observed
TREATMENT:
No known effective therapy for preventing or treating prion diseases
DECONTAMINATION:
- Prions are extremely resistant to most of the common sterilization procedures.
Recommended methods for sterilization of material contaminated with prion proteins are:
1. Autoclaving at 134°C for 1- 1.5 hour
2. Treatment with 1 N NaOH for 1 hour
3. Treatment with 0.5% sodium hypochlorite for 2 hours
- Prions if bound to the stainless steel should be treated with an acidic detergent solution
prior to autoclaving; rendering them susceptible to inactivation
ESSAY 16
CLASSIFY PARAMYXOVIRUSES. WRITE THE MORPHOLOGY, PATHOGENESIS,
CLINICAL FEATURES, LABORATORY DIAGNOSIS, TREATMENT & PREVENTION
OF MUMPS.
SHORT NOTE: DIFFERENCE BETWEEN ORTHOMYXOVIRUS AND
PARAMYXOVIRUS.
MYXOVIRUSES
- Myxo means mucin
- Myxoviruses binds to the mucoprotein receptor on nasopharyngeal
mucosa and in RBC and cause haemagglutination
FAMILY OF MYXOVIRUSES:
PARAMYXOVIRIDAE:
These group of viruses are transmitted via respiratory route and causes
● Localized respiratory infection (influenza virus)
● Spread throughout body causing infection (mumps, measles)
CLASSIFICATION IN PARAMYXOVIRIDAE FAMILY:
SUBFAMILY GENERA MEMBERS LARGE gp F p Hemolysin

PARAMYXOVIRI RESPIROVIRUS PARAINFLUENZA 1,3 HN type + +
NAE RUBULAVIRUS MUMPS, HN type + +
PARAINFLUENZA 2, 4a,4b
MORBILLIVIRUS MEASLES H type + +
HENIPAVIRUS *HENDRA/NIPAH G type + Not identified
PNEUMOVIRINA PNEUMOVIRUS RESPIRATORY G type + -
E
SYNCYTIAL VIRUS
METAPNEUMO HUMAN G type + -
VIRUS METAPNEUMOVIRUS
Abbreviations:
HN – have both hemagglutinin and neuraminidase activities;
H – have only neuraminidase activity;
G – do not have both hemagglutinin and neuraminidase activity;
gp – glycoprotein;
f p – fusion protein
*Only the GENERA OF ZOONOTIC PARAMYXO VIRUSES including nipah and hendra viruses infect
mostly bats, occasionally infecting humans. All other genera are pathogenic to humans
DIFFERENTIATION BETWEEN PARAMYXOVIRUSES AND ORTHOMYXOVIRUSES
PROPERTIES ORTHOMYXOVIRIDAE PARAMYXOVIRIDAE

Size 80-120nm 100-300nm
Shape Spherical, Rarely Pleomorphic
Filamentous
Nucleic Acid Negative Sense Ssrna, Segmented, Negative Sense Ssrna,
Eight Pieces Unsegmented, Single Piece
Genetic Stability Variable Stable

Genetic Recombination Seen Not Seen
Site For Rna Replication Nucleus Cytoplasm
Antigenic Variation Seen Not Seen
Important Human Influenza Virus Parainfluenza Virus, Mumps,

Pathogens Rsv, Measles,
Metapneumovirus
Antigens (Ha/Na) Both Ha And Na Spikes Are Ha Spike Present In- Parainfluenza,
Present, Hemagglutination Is Measles, Mumps
Reversible (Elution Is Seen) Na Spike Present In- Parainfluenza,
Mumps Inclusion Body-
Intracytoplasmic (Exception
Measles It Is
Both Intracytoplasmic And
Intranuclear)
MUMPS
MORPHOLOGY:
Reference: Essentials of Medical Microbiology, Apurba S Sastry E/2 Page No.

501 Fig. 44.5
Shape: Pleomorphic
Size: 100-300nm
RNA:
● Non – segmented
● Negative sense ssRNA
● Helical symmetry and surrounded with nucleocapsid
VIRAL PROTEINS:
6 Structural proteins
1. FUSION PROTEIN- Have the role of syncytium formation and hemolysin activity
2. HN GLYCOPROTEIN - Has both activity of
● Hemagglutinin (binds to sialic acid receptors on epithelial cells and cause viral entry)
● Neuraminidase (degrades sialic acid receptors on host cells and helps release of viral
particle form infected cells)
3. MATRIX PROTEIN-
● Protein shell layer for protection
● Ion channels for transport
ENVELOPE: Made of lipid, has H and N glycoprotein embedded in it
PATHOGENESIS:
CLINICAL FEATURES:
● INCUBATION PERIOD – 19days (Range 7-23)
TREATMENT:
▪ Treatment is mostly symptomatic
▪ Mumps’ immunoglobulin is available, but is not effective, hence not recommended.
PREVENTION:
VACCINES:
● Live attenuated vaccine is followed worldwide
● Trivalent MMR: Live attenuated measles-mumps-rubella
● Quadrivalent MMR: Additional varicella vaccine
● Monovalent mumps vaccines are not commonly used
● SCHEDULES: 2 Doses subcutaneously at 1yr and4-6yrs
● EFFICACY: About 88% after 2 nd dose. Long term immunity is unknown
Short Notes and Sets
of Short Notes
Short Notes:
1. Viral haemorrhagic fever (6)
2. Interferon (6)
3. Antigenic drift and shift (5)
4. Chikungunya fever (3)
5. Bacteriophage (2)
6. Kyasanur forest disease (KFD) (2)
7. Coxsackie viruses. (2)
8. Suckling mice – Definition and uses in Virology
9. Rhinovirus infection
10. Hemagglutination inhibition test
11. Yellow fever
12. Specimen collection, transport and lab
13. Antiviral agents
14. Cutaneous and genital warts
Sets of Short notes:

● SSN 1:
1) Viral diarrhoea (4)
2) Rota Virus (3)
3) Viral gastroenteritis
● SSN 2:
1) Viral replication
2) Viral multiplication
Both 1 & 2 have similar answers.
3) Viral hemagglutinin
● SSN 3:
1) Epidemic keratoconjunctivitis
● SSN 4:
1) Hepatitis E
2) Type C hepatitis
● SSN 5:
1) Mechanism of viral oncogenesis
2) Oncogenes
3) APUD cell tumors
● SSN 6:
1) Latent viral infections
2) Congenital viral infection
Short Notes
SN1: VIRAL HAEMORRHAGIC FEVER
- Haemorrhagic manifestations may occur in patients suffering from several virus
infections.
1. Exanthematous fevers
▪ Smallpox
▪ Chicken pox
▪ Measles
2. Mosquito borne diseases
▪ Yellow fever
▪ Dengue
▪ Chikungunya
3. Tick borne fevers
▪ Kyasanur forest disease (KFD)
▪ Omsk hemorrhagic fever
▪ Crimean – Congo haemorrhagic fever
4. Arenaviruses
▪ Lassa fever
▪ South American haemorrhagic fever
5. Filoviruses
▪ Marburg virus
▪ Ebola virus
6. Hantaviruses
▪ Hantaan virus
▪ Belgrade virus
▪ Seoul
SN2: INTERFERONS
● Proteins of cytokine family
● Produced within hours in response to viral infection
● Role in innate antiviral immune response
● Modulate humoral and cellular immunity
● Have broad cell growth regulatory activities
ANTIVIRAL EFFECTS
● Non – specific defence of host against viral infection
● Interferon itself is not the antiviral agent, it moves to other cells, induces an antiviral
agent
● Does not protect virus infected cells
● Always host species specific in function / not specific for a given virus
● Inhibits replication of wide variety of DNA and RNA virus
● Extremely potent. Very small amount fewer than 50 molecules of interferons per cell are
sufficient to induce antiviral state
If IFNs are added to cells before infection, there is marked inhibition of viral replication
SN3: ANTIGENIC DRIFT AND SHIFT
Antigenic drift Antigenic shift

Minor antigenic changes in either Major antigenic changes in HA or NA, resulting
haemagglutination (HA) or neuraminidase in emergence of new subtype unrelated
(NA) or both. antigenically to predecessor strains.
Gradual sequential change occurring regularly Abrupt, drastic, discontinuous variation in
at frequent intervals. antigenic structure.
Change results due to mutation and selection. Change results from gene reassortment
(recombination) in doubly infected cells.
Accounts for periodic episodes of influenza. Widely spread causing major epidemics or
pandemics.
New antigens, though different from previous Antibodies to the predecessor virus cannot
antigens, are still related to them, so that neutralize the new variants.
antisera to the predecessor virus strains react
with mutant to a certain extent.
SN4: CHIKUNGUNYA FEVER
Re-emerging disease characterized by fever with arthralgia.
VECTOR: Aedes aegypti
SYMPTOMS:
● Sudden onset of fever – Typically biphasic with a period of remission after 1-6 days
● Crippling joint pain
● Lymphadenopathy
● Conjunctivitis
● Maculopapular rash – Common
● Hemorrhagic manifestation – Rare
● Chikungunya cannot be differentiated from uncomplicated dengue
REASONS OF RE-EMERGENCE:
● New mutation (E1-Alanine 226Valine) Alanine in 226th position of E1 glycoprotein
gene is replaced by Valine
● New vector – Aedes albopictus
DIAGNOSIS:
i) Detection of IgM or IgG in paired serum sample – ELISA
ii) To detect viral RNA – RT PCR
TREATMENT: No vaccine is available.

SN5: BACTERIOPHAGE
Bacteriophages: Viruses that attack bacteria
MORPHOLOGY:
▪ Typically, tadpole-shaped possessing a hexagonal head and a tail attached with
tail fibers.
▪ Hexagonal head contains tightly coiled dsDNA, enclosed by capsid (protein coat)
Altered morphology may be seen in some phages:
▪ Shape: Spherical or filamentous instead of hexagonal.
▪ Nucleic acid: May contain ssDNA or RNA instead of dsDNA.
LIFE CYCLE TYPES:

1. LYTIC PHASE: Phage replicates in cytoplasm and lyses host bacteria to come out.
It resembles the replication of other DNA viruses; except:
● In penetration step: Phages are attached to bacterial cell walls as ghosts.
● There is no Uncoating step as seen with other viruses.
● Release of the daughter phages occur by lysis of the host bacterium.
● Duration of Eclipse phase is about 15 to 30 minutes; in contrast to 15-30 hours for most
of the animal viruses.
2. LYSOGENIC OR TEMPERATE PHAGE: Phage DNA is incorporated within host DNA and
remains dormant as prophage.
LYSOGENIC TO LYTIC INTERCONVERSION: When the temperate phages want to come out,
they get excised from bacterial chromosome, then transform to lytic phages, multiply in the
cytoplasm and are released by lysis.
Uses:
1. Phage typing: Phage typing is employed for typing the following bacteria:
Ex. Vi antigen typing of Salmonella typhi
2. Phage assay: To estimate the no. of viable phages in preparations.
3. Used in treatment (Phage therapy): Lytic phages can kill the bacteria, hence may be
used for treatment of bacterial infection, such as post-burn and wound infections.
4. Used in diagnosis: Mycobacteriophages are used for the identification of Mycobacterium
tuberculosis.
5. Used as a cloning vector.
6. Transduction: In Staphylococcus aureus, the plasmids coding for β-lactamases are transferred
between the strains by transduction.
SN6: KYASANUR FOREST DISEASE (KFD)
● Identified in 1957 from monkeys from the Kyasanur Forest.
EPIDEMIOLOGY:
• Vector: Hard ticks (Haemaphysalis spinigera) are the vectors of KFD virus and once
infected, they remain infected for life.
• Hosts: Monkeys, rodents and squirrels are common hosts which maintain the virus through
animal-tick cycles. Reservoirs are the rats and squirrels.
Amplifier hosts are the monkeys, where the virus multiplies exponentially. Man is an incidental
host and considered as a dead end.
• In monkeys: KFD virus has been a cause of epizootics with high fatality in primates especially
in monkeys, hence known as Monkey's disease.
• Situated in India: KFD is currently endemic in five districts of Karnataka.
There is a declining trend of incidence after the initiation of vaccines.
CLINICAL MANIFESTATION IN HUMANS:

• Incubation period varies from 3-8 days.
• First stage (haemorrhagic fever): It starts as acute high fever with malaise and frontal
headaches, followed by haemorrhagic symptoms, such as bleeding from the nasal cavity, throat,
and gums, as well as gastrointestinal bleeding.
• Second stage in the form of meningoencephalitis may occur 7-21 days after the first stage.
Diagnosis is made by virus isolation from blood or by IgM antibody Detection by ELISA.
• Recently, nested RT-PCR and real time RT-PCR have been developed detecting viral RNA
(NS-5 non coding region) in serum samples and can provide early, rapid and accurate diagnosis
of die infection.
• Non-specific findings such as leukopenia, thrombocytopenia and decreased haematocrit,

albuminuria and abnormal CSF are found in the second stage.
KILLED KFD VACCINE:

A formalin-inactivated chick embryo vaccine has been developed for KFD.
• Schedule: two doses at intervals of 2 months, followed by booster doses at 6-9 months and
then every 5 years.
SN7: COXSACKIE VIRUSES
Family: Picornaviridae
Sub family: Enterovirus
● ssRNA, non - enveloped virus
● Infects only suckling mice and not adults
● Incubation period 2-9 days in humans
● Two groups – based on pathological changes in suckling mice & neutralization tests
1. A group –has 24 serotypes
2. B group– has 6 serotypes
● B groups share common complement fixing antigen
A GROUP.
▪ Inoculated in suckling mice
▪ Generalised myositis
▪ Flaccid paralysis
▪ Leads to death within a week
B GROUP
▪ Inoculated in suckling mice
▪ Patchy focal myositis
▪ Spastic paralysis
▪ Necrosis of brown fat
▪ Often results in hepatitis, pancreatitis, myocarditis, encephalitis
HOST RANGE AND CULTIVATION:

● Isolation of the virus and inoculation into suckling mice by intracerebral or subcutaneous
or intraperitoneal routes
● All coxsackie B groups grow well in monkey kidney cell culture while only A7 and A9
of group A virus grows in it
CLINICAL FEATURES OF GROUP A VIRUS:

● Herpangina (vesicular pharyngitis)
● Common in children
● Caused by A2, A6, A8 & A10 virus
● Severe febrile pharyngitis with headache, vomiting, pain in abdomen
● Characteristic lesions: Small vesicles on fauces and on posterior pharyngeal wall, which
breaks to form ulcers
● Aseptic meningitis
● Mostly caused by group A and all group B viruses
● Characterised by presence of maculopapular rash
● HAND FOOT AND MOUTH DISEASE (HFMD)
● Exanthematous fever
● Affects mainly young children
● Characterised by clusters of papulovesicular lesions in skin and oral mucosa
● Mainly caused by coxsackie A16, A9 and B1-3 viruses
● Benign illness resolving in 1-2 weeks
● Minor respiratory infections
● Similar to common cold
● Caused by A10, A21, A24 &B3 viruses
● Acute hemorrhagic conjunctivitis
● Caused by A 24 virus
● Self-limiting subconjunctival haemorrhage
● Incubation period – 1 day / complete recovery within 8-10 days
● Has explosive epidemics among adults in 1969-71 in Africa, South East Asia
CLINICAL FEATURES OF GROUP B VIRUS

● Bornholme disease (epidemic myalgia/pleurodynia)
● Febrile disease with sharp piercing pain in chest and abdomen
● Myocarditis & pericarditis
● Most common in newborn – high fatality
● Sometimes in older children and adult
● Juvenile diabetes
● Most commonly caused by B4 virus
● Orchitis – inflammation of testis
● Transplacental & neonatal transmission
● Resulting in serious disseminated diseases including
● Hepatitis, meningoencephalitis, adrenocortical involvement
● Post viral fatigue syndrome
● Generalised diseases of infants – affects multiple organs
1. ANIMAL INOCULATION:
▪ Virus isolated from lesions / fauces
▪ By inoculating into suckling mice intracerebrally
▪ Group A virus produce flaccid paralysis
▪ Group B virus produce spastic paralysis
2. TISSUE CULTURE:
- All serotypes do not grow in cell lines hence tissue culture is not useful
3. SERODIAGNOSIS:
- As there are existence of several antigenic types, this will also not be useful
4. SEROLOGY: Performed to detect neutralizing antibodies
5. PCR TARGETING SPECIFIC GENES is highly useful as it is rapid, more sensitive,
serotype specific.
EPIDEMIOLOGY:
▪ Primarily coxsackie viruses inhabits alimentary canal
▪ Spreads by feco – oral route
▪ Coxsackie B virus shows epidemics in every 2-5 years
SN8: SUCKLING MICE – DEFINITION AND USES IN
VIROLOGY
- Very susceptible to coxsackie and arboviruses, many of which do not grow in any other
system.
- Method for cultivation of viruses via animal inoculation.
- Earliest methods – Using human volunteers
Now – Using lab animals (mice)
ROUTES OF INOCULATION:
1. Intracerebral
2. Subcutaneous
3. Intraperitoneal
4. Intranasal.
OTHER ANIMALS USED: Guinea pigs, rabbits and ferrets.
INDICATIONS OF GROWTH OF VIRUS:

1. Death
2. Disease
3. Visible lesions
DISADVANTAGES:
1. Immunity may interfere with viral growth
2. Animals often harbour latent viruses.
OTHER USES:
Study of -
1. Pathogenesis,
2. Immune response,
3. Epidemiology
PATTERNS SEEN IN DIFFERENT VIRUSES:
1. Coxsackieviruses:
a) Group A viruses:
Produce generalized myositis and flaccid paralysis, leading to death within a week.
b) Group B viruses:
Produce patchy focal myositis, spastic paralysis, necrosis of brown fat and, often,
pancreatitis, hepatitis, myocarditis and encephalitis.
2. Arboviruses (e.g., Togaviridae, Flaviviridae, etc):

Upon intracerebral inoculation, the animals develop fatal encephalitis. Though serial blind
passages may be necessary in some cases.
SN9: RHINOVIRUS INFECTION
- Also known as Common cold
RHINOVIRUSES:
▪ Human rhinoviruses consist of 3 species (A, B and C)
▪ More than 150 serotypes are found
▪ Use host ICAM-I as receptor
▪ They belong to enteroviruses except
CLINICAL FEATURES:
● Incubation period is about 2-4 days
● Sneezing, nasal discharge, nasal obstruction, sore throat and no fever
● Primary disease presents as RHINOSINUSITIS
Secondary bacterial infection in children may cause otitis media, sinusitis, bronchitis or
pneumonitis
▪ Viruses can be grown in WI-38 and MRC-5 cell lines
▪ Organ culture of ferret and human tracheal epithelium may be necessary in fastidious
strains
TREATMENT: Symptomatic treatment

SN10: HAEMAGGLUTINATION INHIBITION TEST
- Type of neutralization test

- Once used for the diagnosis of viral diseases like influenza
PRINCIPLE:
Anti-H antibodies present in the patient’s sera agglutinates the haemagglutinin
antigen present in viruses.
+ +
PROCEDURE:
▪ In this procedure the flu infected person’s serum containing the anti-HA antibodies
are made to react with the flu virus containing HA surface antigens.
▪ The flu virus has the ability to cause agglutination of human RBCs. Because the
virus has been already attacked by the antibody of the patient’s serum, the virus will
not be present to clump the RBCs, and hence the RBCs will settle at the bottom in
the form of a button.
▪ By calculating the amount of serum required to prevent agglutination of RBC we can
quantify the severity of infection that is expressed in terms of HI titres.
SN11: YELLOW FEVER
➔ It is an acute, febrile illness caused by yellow fever virus.
➔ In severe cases it is characterized by liver dysfunction which leads to jaundice, renal
dysfunction, haemorrhage and mortality.
➔ It is endemic to West Africa and Central South America.
YELLOW FEVER VIRUS

▪ Arbovirus
▪ Belongs to family Flaviviridae
▪ Enveloped virus, containing single stranded RNA (ssRNA).
TRANSMISSION:
➔ Vector for infection in humans is by the bite of Aedes aegypti or the tiger mosquito.
➔ Transmission cycle:
▪ Jungle cycle: It occurs between monkeys and forest mosquitoes
▪ Urban cycle: it occurs between humans and Aedes aegypti.
▪ Incubation period - 3-6 days
▪ In early stage of disease
➔ Presence of fever, chills, headache, dizziness, myalgia and backache followed by
nausea, vomiting and bradycardia.
➔ Infected person is viremic in this stage.
▪ In severe cases
➔ Haemorrhage
➔ Platelet dysfunction
➔ Renal dysfunction
➔ Hepatitis- Torres bodies (intranuclear inclusions inside hepatocytes), jaundice
seen
➔ Mortality rate is high (mainly in children and elderly)
➔ Serology: IgM ELISA
➔ Molecular method: RT-PCR (more confirmatory)
EPIDEMIOLOGY:
▪ Majority of outbreaks occur in Africa
▪ All age groups are susceptible
▪ In India strict guidelines for vigilance and quarantine of travellers in the international
airports is the reason for absence of yellow fever
YELLOW FEVER 17D VACCINE

▪ Live attenuated vaccine
▪ It is prepared in allantoic cavity of chick embryo
▪ Dosage: single dose, given subcutaneously
▪ Vaccine is effective within 7 days of administration
▪ Efficacy lasts for up to 35 years
Contraindications of yellow fever vaccine:
➔ Children < 9 months
➔ Pregnancy (except during outbreak)
➔ HIV infected people
➔ People with allergy to egg
SN12: VIRAL SPECIMEN COLLECTION, TRANSPORT AND
LABORATORY DIAGNOSIS
SPECIMEN COLLECTION:
○ Specimens can be collected from the patient in the forms of swabs, sputum, urine,
aspirates, tissue specimens, body fluids, scrapings (like corneal scrapings) and by
stool collection from the respected infected areas.
○ These specimens are transported in viral transport media.
○ Viral transport media prevents drying of the specimen, maintains
viability of the viruses and prevents overgrowth by
contaminating flora.
○ The specimen should be held at 4°C during transport for most viral specimens.
○ These specimens should not be transported in FORMALIN as they cut and
destroy the DNA into small pieces.
SPECIMEN TRANSPORT:
○ Most of the specimens should be transported within 2 hours.
○ In cases of CSF, Body Fluids - Immediate transport is required.
○ In Urine, Rectal swabs - If with added preservatives like . .
boric acid transport duration is . . acceptable
up to 24 hours.
○ In cases of stool culture - Without medium - 2 hours
With medium - 24 hours is . .
acceptable (Cary-Blair medium)
○ After receiving the specimen, tests are proceeded as fast as possible to achieve
rapid diagnosis.
○ The tests can be in the form of microscopical, staining, immunological,
serological or by molecular methods.
○ The results of the tests must be conveyed to the treating physician who has
requested the investigation and must be conveyed in standard reporting formats
in such a way that the physician or patient is able to get accurate and reliable
results which are clear and easy to understand.
○ A wrong report or an incomplete one might put the patient in danger of wrong
treatment or inadequate management.
SN 13. ANTIVIRAL AGENTS
Reference: Baveja Textbook of Microbiology- Fifth Edition Page No. 432

SN 14: CUTANEOUS AND GENITAL WARTS
➔ Caused by human papillomavirus (HPV)
▪ DNA virus
▪ Non – enveloped, have icosahedral capsids and contain circular double stranded
DNA
▪ Belongs to papillomavirus family
▪ Has selective tropism for Epithelium of skin and mucous membrane
▪ Has more than 100 serotypes
▪ They can produce infections ranging from benign warts to malignant neoplasia of
the cervix.
CUTANEOUS WARTS:
➔ Small, hard, rough growth on skin
➔ It is of following types
● Common skin warts (verruca vulgaris) - common in children
● Flat warts (verruca plana)- common in children
● Plantar warts (verruca plantaris)- common in adolescents
ANOGENITAL WARTS (CONDYLOMA ACUMINATUM):

➔ Caused by serotypes types 6 and 11 of human papillomavirus
● Have low malignant potential
➔ Found in genital area such as
● Penile shaft
● Scrotum
● Labia majora of the vagina
● Anal area
➔ Generally pink in colour
➔ Project out from surface of the skin
➔ Size may vary (from small to large masses)
▪ Most lesions are visible to naked eye. 5% acetic acid solution is applied to
improve visibility
▪ Molecular methods: PCR
TREATMENT:
▪ Removal of the lesion by
● Cryosurgery
● Electrodesiccation
● Surgical excision
● Laser therapy
▪ Topical preparations of
● Interferon, podophyllum used for genital warts.
PREVENTION:
● HPV vaccine
● Barrier method of contraception (prevention of anogenital warts)
Sets of Short notes
SSN 1
1) VIRAL DIARRHOEA
2) ROTA VIRUS
▪ Rotaviruses are the most common cause of Diarrheal illness in children.

▪ Rotaviruses have icosahedral symmetry.
▪ Surrounded by a triple layered capsid.
▪ Possess segmented dsRNA (11 segments)
▪ Proteins: There are six structural viral proteins (VP1 to VP7 except VP5) and six
non-structural proteins (NSPI 6).
PATHOGENESIS:
▪ Rotaviruses infect and ultimately destroy the mature enterocytes in the villi of the
proximal small intestine; however, the gastric and colonic mucosa are spared.
▪ They multiply in the cytoplasm of enterocytes and damage their transport mechanisms
resulting in secretory diarrhoea.
▪ The non-structural protein-NSP4, acts as enterotoxin and induces secretion by altering
epithelial cell function and permeability.
The incubation period is about 1- 3 days. It has an abrupt onset, characterized by vomiting
followed by watery diarrhoea, fever and abdominal pain.
• Direct detection of virus: Faeces collected early in the illness is the most ideal specimen.
Rotaviruses can be demonstrated in stool by lmmuno Electron microscopy (lEM). Rotaviruses
have a sharp edged triple shelled capsid; look like the spokes grouped around the hub of a wheel.
Reference: Essential of Medical Microbiology, Apurba Sastry E/2 Page No. 547 Fig. 49.3
• Detection of viral antigen in stool by ELISA and latex agglutination-based methods.
• RT-PCR is the most sensitive detection method for detection of rotavirus from stool.
VACCINE: Rotavac and Rotarix are available.
3. VIRAL GASTROENTERITIS
Viral etiology accounts for the most of the acute infectious gastroenteritis worldwide.
Viral gastroenteritis most commonly occurs among children.
Persons of all ages can be affected. Several enteric viruses can cause acute gastroenteritis in
humans, most common being rotavirus.
Reference: Essentials of Medical Microbiology, Apurba Sastry E/2 Page No. 546 Table 49.
SSN 2
1. VIRAL REPLICATION
2. VIRAL MULTIPLICATION
Viruses do not undergo binary fission (seen in bacteria), but undergo complex ways of cell
division.
Replication of viruses passes through six sequential steps:
i) Adsorption/attachment:
▪ First and most specific step of viral replication.
▪ Involves receptor interactions between virus and host.
ii) Penetration
After attachment, virus particles penetrate into host cells either by:
▪ Phagocytosis (Viropexis) – through receptor-mediated endocytosis
▪ Membrane fusion – seen in HIV
▪ Injection of nucleic acid – seen in bacteriophages.
iii) Uncoating
Capsid is lysed (due to host lysozymes) and nucleus acid is released – this is absent for
bacteriophages.
iv) Biosynthesis of various viral components:
⮚ Nucleic acid
⮚ Capsid protein
⮚ Enzymes
⮚ Other regulatory proteins
Site of nucleic acid replication:
▪ DNA viruses – DNA replication occurs in nucleus (except in Poxviruses)
▪ RNA viruses – RNA replication occurs in cytoplasm (except in Retroviruses and
Orthomyxoviruses)
v) Maturation - Takes place in the nucleus or cytoplasm.
vi) Release
Release of daughter visions occur by:
▪ Lysis of host cells – seen in non-enveloped viruses mad bacteriophages
▪ Budding through host cell membrane – seen in enveloped viruses
ECLIPSE PHASE:
● Interval between entry of virus into host cell till appearance of first infectious virus particle
● During this period, virus cannot be demonstrated inside the host cell.
● Duration:
▪ Bacteriophages – 15 – 30 minutes
▪ Most of the animal viruses – 15 – 30 hours
3. VIRAL HAEMAGGLUTINATION
● Large number of viruses contain haemagglutinin spikes (peplomers) on the capsid or
envelope which can agglutinate erythrocytes of different species.
● Viral haemagglutinin (glycoprotein) has special affinity for different glycoprotein located
in receptor areas on the surface of erythrocyte.
PROCEDURE
▪ This test provides a simple and rapid method for detection of viruses in egg or tissue
culture fluid.
▪ When erythrocytes are added to serial dilutions of viral suspension, virus and
erythrocytes collide in the suspension and adhere to each other resulting in
hemagglutination.
▪ Highest dilutions that provide hemagglutination provides the titer.
▪ Erythrocytes which are not agglutinated settle at the bottom in the form of ‘button’,
while agglutinated erythrocytes are seen spread into shield-like pattern.
● Hemagglutination reaction is specifically inhibited by antibody to the virus.
● Hemagglutination inhibition test (HI) – Routinely used for detecting antiviral antibody in
diagnosis and research.
● Some viruses, particularly influenza and parainfluenza viruses also carry on their surface
another peplomer, the enzyme neuraminidase which acts on receptors on erythrocytes and
destroys them – Receptor Destroying Enzyme (RDE).
● Destruction of surface receptors results in reversal of hemagglutination and release of
viruses from the surface of erythrocytes – Elution.
● After elution, receptors are irreversibly damaged and erythrocytes are no longer
agglutinable by that particular virus. The free viruses are unharmed.
Reference: Baveja Textbook of Microbiology – Fifth edition Page No.414

SSN 3:
1. EPIDEMIC KERATOCONJUNCTIVITIS
● Disease is produced by Adenovirus –non enveloped DNA virus, space vehicle-shaped.
● Serious condition that appears as an epidemic.
● Usually caused by type 8 and less often by types 19 and 37.
SSN 4
1. HEPATITIS E
- Caused by hepatitis virus E.

- Enterically transmitted hepatitis affects young adults
Family: Heperviridae
Genus: Hepe virus
MORPHOLOGY:
▪ Small, non-enveloped, icosahedral
▪ +ve sense SSRNA, specific Ag
TRANSMISSION: Contamination of food and water intake
● Incubation period 14 – 60 days
● Self-recovering acute hepatitis
● Pregnant women are more prone
● No chronic or carrier state
HEV HAV
Secondary attacks are less Secondary attacks are more
Affects young adults Affects children
● RT PCR – HEV RNA in stools
● ELECTRON MICROSCOPY - HEV RNA in stools
● ELISA – Serum IgM and IgG anti HEV are seen
TREATMENT: No specific antiviral drugs
PREVENTION: HEV 239 vaccine

2. TYPE C HEPATITIS
- Most common post transfusion hepatitis
- Caused by Hepatitis C virus
Family: Flaviviridae
Genus: Hepacivirus
MORPHOLOGY:
● Spherical, enveloped
● +ve ss RNA virus
● Proteins
▪ Core proteins, E1, E2
▪ NS2, NS3, NS4A, NS4B, NS5A, NS5B
▪ P7 membrane proteins
TRANSMISSION:
● Mostly via contaminated blood, needle stick injury
● From infected Drug addicts who share needles
● Vertical transmission also can occur and not transmitted through lactation
● Incubation period 15-160 days
● Acute hepatitis that spontaneously clears within 12weeks
● Sometimes may become chronic hepatitis, cirrhosis, hepatocellular carcinoma
● Some extrahepatic manifestation
○ Mixed cryoglobulinemia
○ Glomerulonephritis
○ Arthritis and joint pain
● ELISA:
- HCV Ab 3rd generation via antigens NS5 with core protein
- HCV core antigen is tested
● MOLECULAR METHODS
- HCV RNA is detected through real time RT PCR
● Gold standard is liver biopsy
TESTING SEQUENCES:
1. Anti HCV Ab test:
● If +ve, HCV RNA tested for active infection
● If -ve, no action needed
2.Hepatitis C screening:
It is done for
● >18 years, HIV patients
● Pregnant, IV drug addicts
TREATMENT:
● Pegylated interferon + Ribavirin
● Direct acting antivirals
○ NS3/4A inhibitors
▪ Grazoprevir
▪ Paritaprevir
○ NS5B inhibitors
▪ Dasabuvir
○ NS5A inhibitors
▪ Daclatasvir
Both are used as combined regimen for 12- 24 weeks
SSN5
1.MECHANISM OF VIRAL ONCOGENESIS
- Viral oncogenesis is a complex multistep process that takes place over a long period of
time. Oncoviruses are usually not cytolytic; they transduce or activate oncogenes.
Oncogenic viruses transforming host cells can be classified under two types:
ONCOGENIC DNA VIRUSES

● Under the influence of the virus, the host cell undergoes malignant transformation similar
to lysogenic conversion in bacteria.
● The cell is not destroyed nor is a virus produced but there is altered expression of
pre-existing cellular genes (which regulate host cell growth) such as Proto-oncogenes,
Tumor suppressor gene, Apoptosis regulatory genes and DNA repair genes that interfere
with cell cycle causing uncontrolled growth and transformation.
● Two events are necessary for viral transformation: a persistent association of viral
genes with the cell, and the expression of certain viral “transforming” proteins.
● Examples of oncogenic DNA viruses:
a) Human herpesviruses (EBV, HHV-8 or KSHV)
b) Human hepatitis B virus
c) Human Papillomavirus and Polyomavirus
ONCOGENIC RNA VIRUSES

● First, most retroviruses do not kill the host cell, but rather set up a permanent infection
with continual virus production. Second, a DNA copy of the RNA genome is integrated
into the host cell DNA by a virally encoded integrase.
● Retroviruses are known to transform cells by two different mechanisms:
i. ACUTE TRANSFORMING OR DIRECT ACTING RETROVIRUSES:
▪ They are certain animal retroviruses (e.g., Rous sarcoma virus) that carry viral
oncogene which they directly insert into the host chromosome.
▪ Oncogenes encode a protein that interferes with cell signalling that results in
uncontrolled cell proliferation and cell transformation.
ii. SLOW TRANSFORMING OR INDIRECT ACTING RETROVIRUSES:
▪ Viral genome can insert anywhere in the host chromosomes randomly and not
necessarily adjacent to proto-oncogenes.
▪ They do not have viral oncogenes, but possess an additional regulatory gene
(e.g., taxgene for HTLV-1 and tatgene for HIV). These genes induce or alter
the expression of pre-existing genes.
▪ E.g., Transactivating factor (Tax) turns on cellular genes, causing cell
proliferation.
● Examples of oncogenic RNA viruses:
a) Retroviruses
b) Human T-lymphotropic viruses I and II (HTLV-I and -II)
c) Hepatitis C virus
2. ONCOGENES
● Oncogenes or cancer genes are genes which encode proteins that trigger the
transformation of normal cells into cancer cells.
● Oncogenes present on the viral genome are called viral oncogenes(V-onc). These
genes are expressed by recombination between retroviral and cellular genes. More than
30 oncogenes have now been found since the original oncogene was identified in Rous
sarcoma virus (called v-src, where the v stands for viral).
● Oncogenes isolated from cancerous cells are called cellular oncogenes (C-onc). These
genes contain introns characteristic of eukaryotic genes.
● The cellular counterpart of oncogenes present in normal cells (not of viral origin)
are called proto-oncogenes. These genes have some essential functions in normal cells
such as coding for proteins involved in regulating cell growth and differentiation. When
mutated they form oncogenes.
● Transfection is the preferred method of study of oncogenes.
● Examples of few oncogenes:
Viral oncogene Origin Neutral Human gene tumour
V-src Chicken Sarcoma C-src
V-ras Rat Sarcoma C-ras
V-myc Chicken Leukemia C-myc
V-fes Cat Sarcoma C-fes
V-sis Monkey Sarcoma C-sis
V-mos Mouse Sarcoma C-mos
3. APUD CELL TUMOURS

⮚ Amine Precursor Uptake Decarboxylation (APUD) cells are cells with special
characteristics such as:
● High amine content
● Capacity of amine precursor uptake
● Property of decarboxylation
⮚ Tumours arising from these cells are called Apudomas. Since APUD cells have peptide
synthesizing properties, common presentations of these tumours are due to increased
neuro-endocrine secretions. Hence, they are also called Neuro-endocrine Tumours
(NETs)
⮚ NETs can arise in many different areas of the body, and are most often located in
the intestine (called carcinoid tumours), pancreas or the lungs.
⮚ Some tumours under NETs include:
▪ Neuroendocrine tumor of the anterior pituitary
▪ Medullary carcinoma
▪ Pulmonary neuroendocrine tumors (e.g., SLC)
▪ Gastroenteropancreatic neuroendocrine tumors (GEP-NET)
▪ Merkel Cell Carcinoma
▪ Inherited conditions such as (MEN- 1 and 2, Von-Hippel Lindau disease)
MERKEL CELL CARCINOMA
● It is also known as cutaneous Apudoma.
● It can be primary neuroendocrine carcinoma of the skin, primary small cell carcinoma
of the skin, or trabecular carcinoma of the skin
● Merkel-cell carcinoma usually arises on the head, neck, and extremities, as well as in
the perianal region and on the eyelid.
● About 80% of MCC tumor patients are infected with Merkel Cell Virus.
● Merkel Cell virus is a double stranded DNA Oncogenic virus under the class
Polyomaviruses.
● The virus is integrated into the host genome in a monoclonal pattern and the viral
replication takes place in the nucleus of the infected cells.
● Transcription of early genes is performed by host RNA polymerase, which leads to
synthesis of early proteins. The early proteins regulate viral transcription, DNA
replication, cell division, and transformation.
● Merkel Cell Virus is usually inactive in infected patients and the patient only becomes
symptomatic defective immune functions such as malignancy, HIV infection, and
organ transplant patients. Conversely, patients with brisk immune responses have
been shown to have improved prognosis.
SSN6
1) LATENT VIRAL INFECTIONS
- In latent infections, the disease is not produced but the virus is not eradicated from the
host.
- The equilibrium between the host and the parasite is achieved in various ways by
different parasites and hosts.
- A latent viral infection does not cause any noticeable symptoms and can last a long time
before becoming active and cause symptoms.
- The virus may exist in a truly latent non-infectious occult form, possibly as an integrated
genome or an episomal agent, or as an infectious and continuously replicating agent,
termed a persistent viral infection.
● Recurrent herpes simplex and herpes zoster are the examples of latent viral infections
where clinical manifestations appear after prolonged periods of quiescence during which
the virus remains hidden in the nerve root ganglia.
● Persistent tolerant infection occurs when the virus is readily demonstrable in the tissues
of the host but neither the disease nor immune response develops. The host is
immunologically tolerant to the virus as a result of congenital or neonatal infection. Disease
sets in when the tolerance is interrupted.
Example: lymphocytic choriomeningitis of mice.
● The virus may exist as an infectious and continuously replicating agent, termed a
persistent viral infection.
In chronic persistent infections the viruses evade the immune response by several
mechanisms. They are:
a) Generation of cells that escape a cell-mediated immune response.
b) Down regulation of MHC production in infected cells so that they are not recognized and
destroyed by T cells.
c) Infection of cells in immunoprivileged sites such as the brain.
VIRAL LATENCY:
▪ Ability of a pathogenic virus to lie dormant within a cell, denoted as
the lysogenic part of the viral life cycle.
▪ Latent viral infection - type of persistent viral infection which is distinguished from
a chronic viral infection
▪ Latency is the phase in certain viruses' life cycles in which, after initial infection,
proliferation of virus particles ceases. However, the viral genome is not eradicated.
▪ The virus can reactivate and begin producing large amounts of viral progeny without the
host becoming reinfected by new outside virus, and stays within the host indefinitely.
▪ Virus latency is not to be confused with clinical latency during the incubation
period when a virus is not dormant.
▪ The mechanisms of viral latency are:

- Episomal latency
- Proviral latency
- Maintaining latency
EPISOMAL LATENCY
Episomal latency refers to the use of genetic episomes during latency. In this latency
type, viral genes are stabilized, floating in the cytoplasm or nucleus as distinct objects, either as
linear or lariat structures.
Example: Herpes virus family
PROVIRAL LATENCY
A provirus is a virus genome that is integrated into the DNA of a host cell. One of the
best-studied viruses that do this is HIV.
HIV uses reverse transcriptase to create a DNA copy of its RNA genome. HIV latency allows
the virus to largely avoid the immune system. Like other viruses that go latent, it does not
typically cause symptoms while latent. Unfortunately, HIV in proviral latency is nearly
MAINTAINING LATENCY
Both proviral and episomal latency may require maintenance for continued infection and fidelity
of viral genes. Latency is generally maintained by viral genes expressed primarily during latency.
Expression of these latency-associated genes may function to keep the viral genome from being
digested by cellular ribozymes or being found out by the immune system.
Example: latency associated transcripts (LAT) in herpes simplex virus
2) CONGENITAL VIRAL INFECTIONS
- Congenital infections affect the unborn fetus or newborn infant. They are generally
caused by viruses that may be picked up by the baby at any time during the
pregnancy up through the time of delivery.
- The viruses initially infect the mother who subsequently may pass it to the baby either
directly through the placenta or at the time of delivery as the baby passes through the
birth canal.
- Mothers generally do not feel sick with the viruses. Sometimes they have flu-like
symptoms. Even if the mother is known to have a viral illness during her pregnancy, her
immune system may prevent the virus from infecting the fetus or newborn infant.
- Vertical transmission is the natural mode of spread of many tumor viruses. The avian
leukosis virus is transmitted in ovo and murine mammary virus through breast milk.
The more common viruses linked to congenital infections include the Cytomegalovirus (CMV),
Herpes, Rubella (German measles), Parvovirus, Varicella (chickenpox), and Enteroviruses.
Rubella and Cytomegalovirus produce maldevelopment or severe neonatal diseases.
PATHOPHYSIOLOGY:
▪ These infectious agents can cross the placental barrier and spread to the fetus in utero
which can cause fetal loss, the emergence of certain congenital
malformation, prematurity or chronic postnatal infection.
▪ The transplacental spread of these organisms to the fetus might be associated
with chronic infection because of the immaturity of the fetus’ immune system. These
organisms are usually not very virulent and the immune system of the developing fetus
can develop tolerance to them.
▪ If this happens, the fetal immune system will fail to eliminate the infecting organisms and
chronic infection might occur.
DIAGNOSIS:
▪ Diagnosis of congenital infections is difficult in early stages. Most congenital infections
in the fetus and newborn baby are totally silent and asymptomatic. But can be serious and
cause profound damage to the body resulting in birth defects or even death.
▪ It can quietly and slowly damage the body, causing medical and developmental problems
that only show up months or even years later.
▪ Diagnosis of a congenital infection can sometimes be made by the obstetrician or
pediatrician based upon the mother’s symptoms, the baby’s physical findings before (by
ultrasound) or after birth, as well as by blood tests on both mother and baby.
▪ Infants with silent congenital infections may not exhibit disabilities for months or years.
▪ Hence, it is important that all babies born with known or suspected congenital infections
be followed closely to detect signs of developmental problems at the earliest possible age.
▪ Close, early follow-up will permit the introduction of necessary interventional therapies
at the earliest time possible.
COMPLICATIONS DUE TO CONGENITAL INFECTION:
MEDICAL COMPLICATIONS:
- Calcifications in the brain associated with brain damage may be seen with CMV
infections. The brain grows poorly and the head subsequently appears small
(microcephaly).
- Hydrocephalus and groin hernias may also occur. Diabetes mellitus and heart
problems can be seen with congenital Rubella infections. Recurrent eye and skin
infections are typical for Herpes.
DEVELOPMENTAL COMPLICATIONS:
▪ Infants with congenital infections may suffer particular damage to the developing brain
and sensory organs.
▪ Subsequent effects of the infection are quite diverse, resulting in a broad range of
developmental outcomes.
▪ Hearing loss is the most common developmental disability, especially from CMV and
Rubella infections. It may be present at birth or develop later in childhood and be
progressive. Hearing loss may be difficult to detect in infancy.
▪ Visual impairments are common, especially with Herpes and Rubella infections. The
impairments result from the development of cataracts or from actual destruction of the
tissues of the eye.
▪ Mild to severe brain damage may occur, resulting in various degrees of mental
retardation, learning and behavioural disorders, and autism. Special education is
frequently required.
REFERENCES
Ananthanarayan and Paniker’s Textbook of Microbiology
▪ Tenth Edition
▪ Eleventh Edition
Essentials of Medical Microbiology, Apurba Sastry

▪ First Edition
▪ Second Edition
▪ Third Edition
Review of Microbiology and Immunology, Apurba Sastry, Sixth Edition
Sherris Medical Microbiology, Sixth Edition
Baveja Textbook of Microbiology, Fifth Edition
Egg innovations and strategies for improvements by Kateri Bertran, Patti J.

Miller, published in 2017

Virology Micro D&R Agam

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Essays

2. Classify rhabdoviruses, details about rabies virus (6)

3. Classify arbovirus, details about Japanese encephalitis (5)

4. Describe in detail the pathogenesis, laboratory diagnosis, treatment, prevention and

6. Details about EBV (3)

7. Classify picornaviruses. Describe the pathogenesis, clinical features and laboratory

9. Discuss briefly on Immunoprophylaxis of viral diseases. Discuss briefly on viral

10. Discuss various methods for isolation of viruses in the laboratory.

12. Discuss the pathogenesis, clinical features, complications, laboratory diagnosis of

13. Discuss the pathogenesis, clinical features, complications, laboratory diagnosis of

16. Classify Paramyxoviruses. Write the morphology, pathogenesis, clinical Features,

GENERAL FEATURES OF HEPATITIS VIRUSES

Hepatitis B viruses are:

▪ Most widespread, produces acute self-limiting hepatitis which is subclinical or

Three morphologic forms:

1. Spherical forms: Numerous, small (22nm in diameter), made of HBsAg antigen.

Mode of replication of HBV

- Definitive diagnosis based on serological demonstration of viral markers

Serological markers of Hepatitis B:

ACTIVE IMMUNIZATION (HEPATITIS B VACCINE):

▪ Method of preparation: HBsAg antigen is used in baker’s yeast by recombinant

PASSIVE IMMUNIZATION (HEPATITIS B IMMUNOGLOBULIN / HBIG):

▪ Indications: Used immediate protection is required

Vaccine + HBIG for neonates born to HBV infected mother

GENERAL PROPHYLACTIC MEASURES:

CLASSIFICATION (Infecting humans)

HOST RANGE AND CULTIVATION:

1. Prodrome: (Early stage of this disease)

STAGES OF DISEASE IN DOGS:

2. Non – neural vaccines:

TISSUE CULTURE VACCINES:

Virus Manifestation Distribution Vector Reservoir

Chikungunya Fever, arthritis Asia, Africa Aedes aegypti Monkeys

Eastern equine Encephalitis East part of Aedes, Culex Birds

Japanese B Encephalitis South East Asia Culex Pigs, birds

Yellow fever Hemorrhagic West Africa Aedes aegypti Monkeys

Kyasanur forest Hemorrhagic Russia Tick Monkeys and rat

Zika virus Fever and Brazil Aedes aegypti Monkeys

California Encephalitis USA Aedes triseriatus Rodents

Colorado tick Fever, rarely America Tick Rodents

Chandipura virus Encephalitis India Sand fly -

SHORT NOTE: DENGUE VIRUS

● Live-attenuated tetravalent vaccine based on chimeric yellow fever-dengue virus

HUMAN HERPES VIRUS

SUBFAMILY GENUS SPECIES

Alpha Simplex virus Human herpesvirus 1 Herpes simplex virus

Human herpesvirus 2 Herpes simplex virus

Varicellovirus Human herpesvirus 3 Varicella-zoster virus

Beta Cytomegalovirus Human herpesvirus 4 Cytomegalovirus

Roseolovirus Human herpesvirus 5 Human herpesvirus 6

Human herpesvirus 6 Human herpesvirus 7

Gamma Lymphocryptovirus Human herpesvirus 7 Epstein-barr virus

HERPES SIMPLEX VIRUS

HERPES SIMPLEX VIRUS 1 HERPES SIMPLEX VIRUS 2

Transmission occurs through Transmission occurs through

Latency in trigeminal ganglia Latency in sacral ganglia

Young children are affected Young adults are affected

VARICELLA – ZOSTER VIRUS INFECTIONS

EPSTEIN – BARR VIRUS

EBV is transmitted by oropharyngeal contact through infected salivary secretions.

3. Lymphoproliferative disorder (seen among immunodeficient patients, e.g. Duncan

5. Chronic fatigue syndrome

INFECTIOUS MONONUCLEOSIS (KISSING DISEASE):