Introduction to Virology 2023

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Introduction to Virology

dr. Dewi Suryani, MInfectDis

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Learning Objectives

1. Understand the charcteristic and structure of virus

2. Understand the different type and classifications of virus

3. Understand the replication process of different type viruses 4. Understand the basis of virus mutationa and its consequence 5. Understand the different methods to identify and culture virus

Block 2 Introduction to Virology 2023

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Reading Resource

Brooks, G.F, et al, 2013, Jawets, Melncik &Adelberg’s Medical

Microbiology 26

^th

Edition, McGraw Hill, New York (Chapter 26: page

407-427)

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Virus Characteristic and Structure

Blok 2 Tahun 2021

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Differences between

Bacteria and Virus

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One hundred years ago, researchers

couldn’t imagine sub microscopic particles, so they described the infectious agent as contagium vivum fluidum—a contagious fluid

(1798) Edward Jenner, introduced the term virus in microbiology. noticed that milk maids who infected with cowpox develop immunity against smallpox.

He inoculated a boy with the vesicle fluid taken from the hand of infected maid. The boy developed

sustained immunity against smallpox.

(1935) Wendell Stanley, isolated tobacco mosaic

virus TMV, making it possible for the first time to carry out chemical and structural studies on a purified

virus. At about the same time, the invention of the electron microscope made it possible to see viruses.

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Historical Background

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Virus Characteristic

Size

• smallest infection agent (20nm-

300nm)

Genome

• Comprose either DNA or RNA

Metabolisme

• Obligate

intracelullear

• Only able to replicate inside host

• Does not have cytoplasma,

mitochondria and

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From Black, JG: Microbiology: Principles and Explorations, 4th edn, John Wiley & Sons Inc., 1999

Virus Characteristic: Size

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Enveloped virus with icosahedral symmetry Virus with helical symmetry

Virus Characteristic: Structure

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Virus Characteristic: Structure

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Terminologi

Capsid capsomer envelope

nucleocapsid peplomer Virion

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Terminologi

TERMINOLOGY DEFINITION

Nucleocapsid The protein–nucleic acid complex representing the packaged form of the viral genome

Capsid The protein shell, or coat, that encloses the nucleic acid genome Virion The complete virus particle,

-Non Envelope protein : nucleocapsid

-envelope virus : enveloped and nucleocapsid

Capsomeres Repeated subunits that constructs the capsid on the surface of icosahedral virus particles

Envelope -surrounds some virus particles

- lipid bilayer surrounding the capsid of some viruses

Peplomer -Virus-encoded glycoprotein that are exposed on the surface of the envelope

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Virus Genome

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Why are viruses formed by repetitive sub units?

karena struktur simple atau sederhana

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▷ Helical Viruses:

▷ Example: Ebola viruses

▷ Polyhedral Viruses:

▷ Example: poliovirus.

▷ Complex Viruses:

example :bacteriophage.

General Morphology

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Virion Symmetry

TYPES OF CAPSID SYMMETRY RECOGNISE:

HELICAL ICOSAHEDRAL COMPLEX

REGULAR IRREGULAR

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I. Helical

• Spiral arrangement of

capsomers around nucleic acid

• Capsid appears cylindrical

• Eg : Rhabdovirus

→ rabies virus

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II. Icosahedral

• Capsomers are assemble into 20 equilateral triangular faces

• An icosahedron (20 sided solid) is the most economical way to build a

symetrical maximal volume

• Capsid appears sperical

• Eg : Adenovirus

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III.Complex

REGULER

• Capsid have components with both helical and icosahedral symmetry

• E.g. Bacteroiphage IRREGULER

• Non-symmetrucal capsid structure

• E.g. Pox virus

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Size Of Viruses

• Viruses vary in size 20 to 300 nm in diameter.

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Viral Protein

Viral proteins serve several important functions,

• The outer capsid proteins protect the genetic material and mediate the attachment of the virus to specific receptors on the host cell surface.

• Provide structural symmetry of virus particle

• It is also important antigens that induce neutralizing antibody and activate cytotoxic T cells to kill virus infected cells.

• Viruses also have internal viral proteins, essential in the initiation of

viral replication in the host cell, e.g. DNA or RNA polymerases.

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Viral Nucleic Acid -DNA

• Most DNA viruses have double stranded (dsDNA) genomes with the exception of parvovirus which is a ss DNA Virus

• DNA virus genome: 3200 bp – 375.000 bp

• They could either be in a form of:

- Circular genome, e.g. papoviruses - Linear genome, e.g Poxviruses

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Viral Nucleic Acid -RNA

• Almost all RNA are single stranded (SS)

• Genome: 4000 bp – 32.000 bp

• SS viral nucleic acid could be defined by its polarity

DESCRIPTION EXAMPLE

RNA

SS + sense

•Its nucleotide sequence is the same sense as mRNA

•Directly translated by cell machinery

Polio virus Rubella virus RNA

SS - sense

• Its nucleotide seqeunce is complementary to mRNA

•Converts to “plus sense” by encoded RNA dependent RNA polymerase

Measles virus

segmented Viral genes encode by separate RNA molecules Influenza virus

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Viral Lipid Envelopes

• Thick lipid bilayer derived from host cell membrane

• Contain virally encoded glycoprotein

• Essential for viral infectivity → destroying envelope inactivates these viruses

• Envelope viruses are sensitive organic solvent

• Play a major roll in cell entry by fusion

Dasar dasar Virologi Blok 2 Tahun 2021

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Are there any association of the present of envelope virus with mode of transmission

and survival of virus?

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Viral Glycoprotein

• Part of the viral envelope

• Provide role in membrane fusion → glycoprotein part of the envelope that interacts with cellular receptor of the target cell

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Virus Classification

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Nomenclature of Viruses

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Various approaches, (do not obey the binomial nomenclature) derived from:

Named after the diseases

eg. Measles virus, smallpox

virus

Name after the places

where the disease first

reported

eg. Newcastle disease virus, Ebola virus,

Norwalk virus, Bunyaviridae

Host and signs of disease

e.g. Tobacco mosaic

virus,

cauliflower mosaic

virus brome mosaic

virus

Latin and Greek words

e.g.

Coronaviridae – “crown”

Parvoviridae–

“small

Virus discovers

e.g. Epstein- Barr virus

How they were originally thought to

be contracted

e.g. dengue virus (“evil spirit”), influenza virus

(the “influence”

of bad air)

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Classification of Virus

Using International Committee on Taxonomy of Viruses (ICTV) to classify the viruses

cation of V ir u s

1- Classical system

- eg. animal, plant, bacterial virus

- eg. naked or enveloped virus

2- Based on Genomics

Baltimore classification

3- Based on Serology

Classification based on Diagnostic virology

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Baltimore classification

30

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Classification of Virus

BASIS DESCRIPTION

Virion Morphology Size, shape, type of symmetry, capsid

Virus Genome properties Type of nucleic acid (DNA or RNA), strandedness, sense, G+C content

Physicochemical properties Molecular mass, thermal stability, pH stability, susceptibility to physical and chemical agents

Virus protein properties Number, size and functional activities of protein

Genome organization and replication Gene order number of open reading frame, strategy of replication

Biologic properties Natural host range, mode of transmission, vector relationship, pathogenicity

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2.2 Example of DNA Viruses

jenis Contoh

Papillomavirus Contoh: Human Papilomavirus (HPV) dapat menyebabkan “wart” dan carcinoma cervix

Adenovirus Terdiri dari beberapa serotype dan meyebabkan infeksi pada saluran pernafasan, conjungtivitis dan gastroenteritis

Hepadnavirus Menyebabkan akut dan kronik hepatitis

Herpesvirus Human herpesviruses meliputi herpes simplex types 1 and 2 (oral and genital lesions), varicella-zoster virus (chickenpox and shingles), cytomegalovirus, Epstein-Barr virus (infectious mononucleosis and association with human neoplasms), human

herpesviruses 6 and 7 (T lymphotropic), and human herpesvirus 8 (associated with Kaposi sarcoma).

Poxvirus smallpox, vaccinia, molluscum contagiosum

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2.2 Example of RNA Viruses

Jenis Contoh

Picornavirus The groups infecting humans are

- enteroviruses (polioviruses, coxsackieviruses, and echoviruses) - rhinoviruses (> 100 serotypes menyebabkan common colds) - hepatovirus (hepatitis A).

Flavivirus yellow fever virus dan dengue viruses Coronaviruses SARS, MERS-CoV, SARS-COV2

Orthomyxovirus influenza viruses menginfeksi manusia or hewan

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Viruses causing Cancer

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Example of viruses Grouped according to similarity in clinical implication

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2.2 Contoh kondisi klinis

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2.2 Contoh kondisi klinis

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Atypical Viruses

ATYPICAL VIRUSES DESCRIPTION

Defective viruses/satellites composed of viral nucleic acid and proteins but cannot replicate without a helper virus which provide the missing function.

E.g Hepatitis D Virus → Hepatitis B Virus

Pseudovirions Contains host cell DNA instead of viral DNA within the capsid. Formed during infection with certain viruses when the host cell DNA is fragmented and

incorporated within the protein capsid

Viroids consist of single molecule of circular RNA without a protein coat or envelope.Only known to be as plant viruses.

are infectious particles that composed of proteins and contain no detectable

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Virus Replication

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General Steps In Viral Replication Cycle

Attachment

Penetration

Uncoating Assembly

Release

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Virus Life Cycle

1. Attachment is a specific binding between viral capsid proteins and specific receptors on the host cellular surface,

2. Penetration , viruses enter the host cell through receptor mediated endocytosis or membrane fusion,

3. Uncoating , the viral capsid is degraded by viral enzymes or host enzymes thus releasing the viral genomic nucleic acid,

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Virus Life Cycle

4. Replication involves synthesis of viral messenger RNA ) mRNA ( for viruses except positive sense RNA viruses,

5. Viral protein synthesis and assembly of viral proteins and viral genome replication,

6. Viruses are released from the host cell by lysis. Enveloped viruses

(e.g., HIV) typically are released from the host cell by budding.

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Pathways of Entry of Viruses into Host Cells

Fusion Endocytosis

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Virus Life Cycle: DNA Virus

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DNA Virus Biosynthesis

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Virus Life Cycle: RNA Virus

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RNA Virus

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Virus Replication

https://www.youtube.com/watch?v=RO

8MP3wMvqg&t=164s

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Virus Mutation

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Viral Genetics

• Viruses grow rapidly, there are usually a large number of progeny virions per cell.

There is, therefore, more chance of mutations occurring over a short time period .

• Errors that take place during genome replication may be preserved and be amplified

in favorable condition in relation with the viruses survival

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Virus Mutation

Spontaneous mutations

• These arise naturally during viral replication: e.g.

due to errors by the genome-replicating polymerase or a result of the incorporation of automeric forms of the bases.

• DNA viruses tend to be more genetically stable than RNA viruses. There are error correction mechanisms in the host cell for DNA repair, but probably not for RNA.

Induced mutation by physical or chemical means

• Chemical agents : e.g. nitrous acid

• Physical: agents such as UV light or X-rays

https://www.youtube.com/watch?v=qD8dAbov5JU

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How Mutation Occurs?

As like any other viruses SARS-COV2 are obligate intraceluler organisme. Hense require the cell host to replicate. The more

Increase transmission means

increase possibility for the New strains emerge

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Mutation on Segmented Virus:

Influenza Virus

Virus mutation

Antigenic drift/

recombination

where individual bases in the DNA or RNA mutate to other bases

Antigenic Shift/

reassortment

where there is a major change in the

genome of the virus

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Antigenic Drift/Recombination : Influenza virus

• accumulation of point mutation in the surface glycoprotein (HA and NA) of influenza viruses

• Antigenic drift is estimated to occur

approximately every 2-8 years as a response to selection pressure to invade human

immunity

• Causes seasonal influenza

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Antigenic Shift/Reassortment:

Influenza virus

• occurs when a cell is infected by two different influenza A viruses (animal and human

influenza A virus)

• Results in a novel viruses virus particles

inherit a combination of RNA segement from both parental viruses

• Causes major pandemics

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Antigenic Shift/Reassortment: Influenza virus

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Different Variants of SARS-COV2 Classification

Variants of Concern (VOC)

Variants of Interest (VOI)

Variants of High Consequence

(VOHC)

▪ Increase in transmissibility or detrimental change in COVID-19 epidemiology;

OR

▪ Increase in virulence or change in clinical disease presentation; OR

▪ Decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics

▪ Genetic changes that are predicted or known to affect virus characteristic: eg transmissibility, disease severity, immune escape, diagnostic or therapeutic escape; AND

▪ Identified to cause significant community transmission or multiple COVID-19 clusters, in multiple countries with increasing relative prevalence and number of cases over time, or other apparent epidemiological impacts to suggest an emerging risk to global public health.

▪ has clear evidence that prevention measures or medical countermeasures (MCMs) have significantly reduced effectiveness relative to previously

circulating variants

Currently, there are NO SARS-CoV-2 variants that rise to the level of high consequence

(CDC,2021 a; WHO 2021 a)

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Different Variants of SARS-CoV2 Classification

VOI VOC VOHC

as more evidences arises as more evidences arises

dismiss

as more evidences arises

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Different Variants of SARS-CoV2 Classification

WHO label Linage Earliest Document sample detected

Date Designated

VOI

Eta B.1.525 Multiple countries 17-Mar-2021

Iota B.1.526 United States of

America 24-Mar-2021

Kappa B.1.617.1 India

4-Apr-2021

Lambda C.37 Peru 14-Jun-2021

(WHO 2021 a)

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Different Variants of SARS-CoV2 Classification

WHO label Linage Mutation Spike of interest

Earliest Document sample detected

Date Designated

VOC

Alpha B.1.1.7* N501Y, D614G,

P681H United Kingdom 18-Dec-2020 Beta

B.1.351 * B.1.351.2 B.1.351.3

K417N, E484K, N501Y, D614G,

A701V

South Africa

18-Dec-2020

Gamma

P.1*

P.1.1 P.1.2

K417T, E484K, N501Y, D614G,

H655Y

Brazil

11-Jan-2021

Delta

B.1.617.2*

AY.1 AY.2

L452R, T478K, D614G, P681R

India

VOI: 4-Apr-2021 VOC: 11-May-

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Consequence of antigenic change

Amino acid substitutions

that alter epitope

Increasae receptor binding

avidity

Changes in glycosylation

Deletion and

insertion Allosteric

structural effect

A change in epitope residues directly

diminshes Ab binding. Eg.

Neutralizing antibodi forms bridge with spike protein K147

and K150;

replacement of glutamate → lysine has the potential to diminsh Ab Binding

Increase respetor binding cause higher

avidity interaction between glycoprotein

and cellular receptor.

Eg subitution of N501Y increase ACE

binding affinity

Glycans are

molecules that shield epitopes from Ab

binding. Hence substitution provide increase potential to escape the immune

system

Any deletion, insertion inside or outside the eiptope may cause diminsh of

the Ab binding

(Harvey et al, 2021 )

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MUTATION of sars cov-2

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Virus Identification

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Viruses can not be cultivated on artificial culture media.

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“

The fact that viruses can’t multiply outside a living host cell complicates their detection, enumeration, and identification.

✓Viruses must be provided with living cells instead of a fairly simple chemical medium

⁽¹⁾

.

66 Block 2 Introduction to Virology 2023

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Methods for

growing viruses in the

laboratory

solid media plaque method

(detect and count viruses)

liquid media

Living Animals Embryonated Eggs

Cell Cultures

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Growing

Bacteriophages

(2) Growing Animal Viruses

(3) Growing plant

Viruses

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(1) Growing

Bacteriophages in the Laboratory

The Number of Plaques

=

Plaque- forming

Units (PFU).

Figure 4. plaque method. 33

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(2)Growing Animal Viruses

A- In Living Animals :

▷ Some animal viruses can be cultured only in living animals, such as mice, rabbits, and guinea pigs.

▷ Most experiments to study the immune system’s response to viral infections .

▷ Animal inoculation may be used as

a diagnostic procedure for identifying and

isolating a virus from a clinical specimen.

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B- In Embryonated Eggs:

Viral growth is signalled by:

1.

the death of the embryo.

2.

embryo cell damage.

3.

by the formation of typical pocks or lesions on the egg membranes.

5.

70

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B- In Embryonated Eggs :

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C - In Cell Cultures :

Cell cultures have replaced embryonated eggs as the preferred type of growth medium for many viruses. Cell cultures consist of cells grown in culture media in the laboratory

.

72

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(2)Growing Animal Viruses

C - In Cell Cultures :

Cell culture lines are started by treating a slice of animal tissue with enzymes that separate the individual cells (Figure5). These cells are suspended in a solution that provides the osmotic pressure, nutrients, and growth factors needed for the cells to grow.

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74

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Virus Identification

Virus

Identification Cultivation of

Viruses

Quantitation of Viruses

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Cultivation of viruses

Embryonated chicken eggs

e.g. influenza viruses

Cell Culture

Primary cell culture

Derived from animal tissue e.g monkey kidney cells, mouse

Diploid cell strains

Consist of single cell type, retaining the diploid chromosome

Continous cell lines

Derived from tumor cell

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CULTIVATION OF VIRUSES

• Evidence of virus growth are Cytopathic Effect (morphologic changes of the cell):

cell lysis, swelling of nuclei, fragmentation of oragella,

cytoplasmic vacuolation, giant cell

• Not all virus show CPE

• Specific Identification through Molecular based such as PCR

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BACTERIA VS VIRUS CULTURE

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VIRUS CULTURE

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VIRUS CULTURE: CPE

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QUANTIFICATION OF VIRUS

TYPES OF QUANTIFICATION DESCRIPTION EXAMPLE

Physical Methods Not involving tissue culture PCR, ELISA

Biological Methods Involving tissue culture Measurement of CPE in tissue culture or series dilution

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References

• Brooks GF, caroll KC, Butel JS, Morse SA, Mietzner TA. Jawetz, Melnick

& Adelberg's: Medical Microbiology. 25th ed. New York: McGraw Hill; 2010

• Champoux J, Grew Wl, Marcalonid JJ, Neidhardt FC, Plorde JJ, Falow S.

Biology of Viruses. In: Ryan KJ, Ray CG, editors. Sherris Medical

Microbiology: An Introduction to Infectios diseases, 4th Edition ed.

New York: Mc Graw Hill; 2004

• Lustig A, Levine A.J. History of Virology: One Hundred years of Virology. J.Virol 66. 44429-4631

• Nelson MI, Holmes EC. The evolution of epidemic influenza. Nature