Introduction to Virology 1

Introduction to Virology FIV 1987 Pedersen and colleagues

Prion 1982 Stanley Prusiner
World eradication of 2011 WOAH
Discovery of Viruses rinderpest
- Discovery of virologic disease is dependent on the
discoveries of bacteria Biological Nature of Viruses
th
- Led by Hippocrates as early as the 4 century with - Virus are devoid of any functional organelle, thus not
his studies on infectious disease like rabies cells
- First observation of a virus was made possible with - They are heavily dependent on its host
Chamberland filter or Pasteur-Chamberland filter
- Considered inanimate when present in the
- Developed by Charles Edouard Chamberland environment
- Scientist studied was passed through the Characteristic shared by viruses
filter, thus virus was once called filterable - Viral growth and multiplication occur only in
agent living cells
- Have either RNA or DNA but not both
- Tobacco Mosaic Virus was the first known virus
- Cannot grow or undergo binary fission
identified in plants - Make use of the ribosome of their host cells
- Russian Martinus Beijernick and - Reproduce solely from their nucleic acid
Ivanofsky/Ivanoski last 1892 except some satellite viruses which uses the
nucleic acid of a helper or master virus
- Followed by the discovery of animal virus - Lacks genetic information for the synthesis
of essential cellular systems

Year Scientist Viral Structure

Foot and Mouth 1898 Loeffler and Flosch
Disease Virus - Virus are considered the smallest infectious agent
Myxosoma virus 1898 Sanarelli
Yellow Fever Virus Reed and Carroll-
- 20 – 300 nm in diameter
African Horse 1900 M’Fadyean
Sickness Virus
- Consist of nucleic acid which encodes proteins
Fowl Plague Virus 1901 Centanni, Lode, & Gruber
Rabies Virus 1903 Remlinger and Riffat-Bay
- Some have a lipid bilayer membrane (only for
Hog Cholera Virus 1903 DeSchweinitz and Dorset enveloped) acquired from the host cell by budding
Rinderpest 1900s Arnold Theiler
Avian Leukemia virus 1908 Ellermann and Bang - Virion refers to the entire infectious agent, a complete
Poliovirus 1909 Landsteiner and Popper viral particle which serves to transfer viral nucleic acid
African Swine Fever 1910 R. Eustace Montgomery from one cell to another.
Virus
Rous Sarcoma Virus 1911 Rous - Virion are composed of nucleic acid, capsid,
Canine Distemper 1926 Laidlaw and Dunkin and envelope (absent in naked virus)
Virus
Newcastle disease 1927 Doyle Capsid - protein coat or shell
virus - encloses the genome
Swine Influenza Virus 1931 Shope - icosahedral or helical symmetry
Influenza virus – 1933 Andrewes, Laidlaw, Smith,
Isolation & Burnet
- Capsomeres*
Yellow fever vaccine 1935 Max Theiler Nucleocapsid - the capsid with enclosed nucleic
Bovine Viral Diarrhea 1940s Olafson, Pritchard, acid
1950s Gillepsie, Baker and Nucleic acid - either DNA or RNA
colleagues
- linear or helicl
Scrapie and 1950s Sigurdsson
Maedi/Visna - segmented or non-segmented
Inactivated and 1954 Salk and Sabin - positive sense or negative sense
attenuated polio virus and - single-stranded or double-
vaccine 1957 Envelope - lipid membrane that surrounds
Canine Parvovirus 1978 Carmichael, Parrish and
come viral particles
colleagues
HIV 1984 Montagnier and colleagues
 Introduction to Virology 2

- acquired through budding from Helical symmetry is formed due to the repeated
host cell protein-protein interfaces on the structural units,
Capsomeres are morphologic units, polypeptide giving a symmetrical assembly of the helix
clusters on the surface of icosahedral viral particles
Within the nucleocapsid, the genomic RNA forms a
Viral Symmetry spiral
- either icosahedral or helical
- virus differ based on the presence of an envelope
- other viruses are characterized by a complex
structure

Five basic types of Viral Symmetry

- Naked isocahedral
- Envelope isocahedral
- Naked helical
- Enveloped helical Animal virus with a helical symmetry always
- Complex possess an envelope

Virions with icosahedral symmetry have 12 corners, Symmetry of Vertebrate Virus

30 edges, and 20 faces, each face an equilateral Symmetry DNA RNA
triangle. Naked - Parvoridae - Reoviridae
Icosahedral - Papillomariviridae - Birnaviridae
They posses two-, three-, and five-fold rotational - Poluomariviridae - Caliciviridae
symmetry and these axes pass through their edges, - Adenoviridae - Picornaviridae
faces, and vertices respectively. - Circoviridae - Astrovirdae
Enveloped - Hepadnaviridae - Flaviviridae
Icosahedral - Herpesviridae - Togaviridae
- Asfarviridae - Arteriviridae
- Bornaviridae
Naked/ - Iridoviridae
Enveloped
Icosahedral
Enveloped - Coronaviridae
Helical - Filoviridae
- Rhabdoviridae
- Bunyaviridae
-Orthomyxoviridae
Some virions, both hexon and penton share the - Paramyxoviridae
- Arenarviridae
same polypeptide, some do not.
Complex - Poxviridae

Sizes of Viruses
- Poxviridae are the largest animal viruses that can be
viewed under a dark-field microscope
- Circoviridae are the smalles animal virus
- For RNA viruses, Picornaviridae and Astroviridae are
the smallest

Because of these variations in the structural Virus Size in diameter (nm)

arrangement, some virus appears hexagonal while Adenoviridae 70 - 90
others spherical. Arenaviridae 50 – 300
Arteriviridae 50 - 70
 Introduction to Virology 3

Asfarviridae 175 – 215 - these proteins, once aggregated, can form inclusion
Astroviridae 28 - 30 bodies
Bornaviridae 70 – 130
Bunyaviridae 90 – 120 Types of Protein
Structural - Makes up the capsid and other
Carliciviridae 35 – 40
Protein components of a virion
Circoviridae 17 - 22 Non- - Acts as enzyme involved in nucleic acid
Coronaviridae 80 - 160 structural replication, transcription and translation,
Filoviridae 80 x 790 - 14000 shut down of host cell functions, and
Flaviviridae 40 – 50 subversion of host machinery to viral
Hepadnaviridae 42 activity
Herpesviridae 150 - 200 - Examples include replicases,
Iridoviridae 125 - 300 transcriptases, and proteases
Orthomyxoviridae 90 – 120
Papillomaviridae 55 Function of Viral Protein
Paramyxoviridae 150 – 300 1. Determine antigenicity of virus for vaccine
Parvoviridae 18 -26 production
Picornaviridae 28 – 30 2. Determine relatedness of viruses for
Poxviridae 170 – 200 x 300 – 450 diagnostician and classification
3. Protection of viral genome against nuclease
Rhabdoviridae 70 – 85 x 130 – 380
inactivation
Reoviridae 60 – 80
4. Participate in adsorption of viral particle
Retroviridae 80 – 130
5. Provide structural symmetry to virus
Togarviridae 60 – 70
Lipids
Chemical Composition of a Virion - Viral lipids are 20 – 35% of dry weight among
Nucleic Acid enveloped virus

- either DNA or RNA genome - 50 – 60% are phospholipids and the remainder as
- double-stranded or single-stranded cholesterol
- positive-sense or negative-sense - Mostly present as lipid-protein bilayer in enveloped
- linear or circular virus, embedding the virus-coded peplomers (spike
- segmented or non-segmented (monopartite or protein) and other viral proteins
multipartite)
- The composition of the membrane lipids varies with
- Viral nucleic acid is infectious, it can replicate and the particular membrane system employed for virion
produce progeny once experimentally introduced into budding
a cell.
- e.g. if virion buds from golgi, the lipids are
Methods used to Characterize Viral Nucleic Acid similar to those found in the golgi
1. Acidrine orange staining and Fluorescent
Microscopy Carbohydrates
2. Uranyl Acetate Staining
3. Electron Microscopy - Carbohydrates occur as oligosaccharide side chains
of viral glycoprotein, glycolipids, and muco-
Positive - Viral genome has the same sense or polysaccharide (envelope)
Sense nucleotide sequence as mRNA - Carbohydrate synthesis is controlled by virus and
- can directly be used for protein
host cell genome
synthesis
Negative - genome is complementary to mRNA - Similar with proteins, they function as antigenic
Sense determinants
Protein
- viral protein ranges from 1 to >100 Stability of Viral Infectivity

- Virus are more sensitive than bacteria or fungi to
physical and chemical agents
- Knowledge to viral sensitivity to environmental
conditions is important in;
- Vaccine production by ensuring viral
infectivity is preserved; and
- Inactivation via sterilization, disinfection and
in vaccine production
Effect of Temperature
- Major environmental condition that may adversely
affect viral infectivity
- Few minutes at 55 – 60°C, surface proteins are
denatured rendering virions unable to attach to
receptors, penetrate the cell, and uncoat.
- Enveloped virus are less stable than naked virus
even at -90°C
- Ice crystal formation leads to virion disruption
making enveloped virions more vulnerable to
repeated freezing and thawing.
- Lower temperature, longer half-life of virus
Half-life: the time required to reduce the concentration
to half its original value
Means of Preservation of Virus
Short term - Refrigeration at 4°C
Long term - Use of dry ice (-70°C)
- Use of liquid nitrogen (-196°C)
Two ways to maintain virus stock in the laboratory
a. Virus stock can be prepared in small aliquots
and rapidly frozen using dimethyl sulphoxide
(DMSO). Stored at -70°C ot -196°C
b. Lyophilization followed by storage at 4°C or
-20°C
Effect of pH
- Isotonic environment and physiologic pH preserves
viruses
- Some virus have narrow ionic and pH tolerance
- Some can tolerate wide ionic and pH ranges
- Most enveloped virus are killed in stomach acid (pH
5-6)
- Enteric virus such as rotavirus and picornavirus can
survive stomach acid
Introduction to Virology 4
Stabilization of Salts
- Virus can be stabilized by salt at 1mol/L
concentration
- They are not inactivated even by heating at
50°C for 1 hour
- The role of salts in viral stability is important in
vaccine development
Examples of preferential stabilization of viruses
by salt
1M Magnesium Chloride - Picornavirus
- Reovirus
1M Magnesium Sulfate - Orthomyxovirus
- Paramyxovirus
1M Sodium Sulfate - Herpes Simplex virus
According to a study, Equine Herpesvirus Type 1
can survive in a wide range of salt concentration.
High salinity preserves viral DNA at the expense of
viral infectivity
Antibiotic Sensitivity
- Viral infection are often complicated by bacterial
infection
- Bacteria can promote viral fitness by
enhancing virion stability, promoting infection
of eukaryotic cells, and increasing coinfection
rates
- This may increase disease severity or
prolonged recovery period
- E.g. Aquabirnavirus do not normally cause
symptoms among fishes, but when coinfected
with Erdwardsiella tarda or Streptococcus iniae
the mortality rate increases
- Viral-bacterial interactions are implicated in the
pathogenesis of autoimmune disease like uveitis and
respiratory infections like influenza and SARS-CoV2.
- This justifies the use of antibacterial in viral
infection
- Rifampin or rifampicin possess both antibacterial and
antiviral activity.
- In poxvirus, rifampicin prevents scaffolding
protein (D13) to nascent viral membranes,
thereby inhibiting virion assembly. This action
is independent of it antibacterial property which
 Introduction to Virology 5

targets bacterial DNA-dependent RNA Latent - Period between infection and onset of
polymerases. Period symptoms
- New or progeny virions are produced
Chemical Agents - stages of life cycle of a virus in latency are
uncoating, replication, and maturation
- Chemical inactivants must be avoided since they - followed by a long plateu (represented by
destroy the infectivity of enveloped virus release of progeny from infected cells)

- including Ether, Chloroform, Aldehydes,

Ethylene oxide, Urea, Phenol, and Detergents
- Selection of disinfectant depends on its spectrum of
activity, human safety, and effect on animal health and
behavior
Non-ionic - possess high virucidal effectiveness
surfactants against;
- Herpesvirus, Retrovirus,
Orthomyxovrius
- Togavirus, Parmyxovrius, Flavivirus
- Rhabdovirus, Bunyavirus, Coronavirus
- High virucidal activity correspondes to
high cytotoxicity General steps in viral replication cycle include
Formaldehyde - reacts with viral nucleic acids adsorption, penetration, uncoating, maturation, and
- destruction of viral infectivity release.
- commonly used in production of
inactivated vaccine* 1. Adsorption or Attachment
- Single-strand are more readily
inactivated compared to double-strand - Virus attaches itself to host cell.
Detergents - Nonident p40, X-100, Sodium dodecyl
sulfate - This involves binding of a viral particle to cell
- solubilize lipid constituents of viral surface molecule (ligand-receptor binding)
membranes
- Used in vaccines or for chemical - Molecule responsible are also known as
analysis attachment factors, entry factors, receptors,
*because of its minimal adverse effect on the co-receptors, or viral receptors
antigenicity of viral proteins
- Some virus attach to only one type of receptors,
others may attach to several different receptors
Viral Genetics and Replication - Knowing the location of these host cell
receptors can pinpoint target tissues or organs of a
Virus can only multiply on living cells. Cells provide the
specific viral particle.
energy and machinery for viral synthesis of nucleic
acid and protein. Target Host Receptors of Veterinary Important
Viruses and their Location in the Host
Virus replicate uniquely, viral particles are synthesized Virus Virus Host Receptor Location of
anew from structural ad non-structural components Particle Receptor
Rabies virus G Nicotinic acetycholine PNS and CNS;
encoded by different viral genes. receptors (nACHr) Neuromuscular
junction
Viral growth cycle is a one-step growth curve, different Chikungunya E2/1 or Mxra8 Fibroblast;
from bacteria. virus E3/2 skeletal muscle
cells;
chondrocytes
Eclipse - sudden disruption of its infectivity in viral life E2 Glycosaminoglycans ECM, CT,
period cycle (GAGs, such as basement
- no virion is detected heparin sulfate) membrane of
- virus enters the cell, uncoats then replicate cartilage and
skin
its nucleic acid. HIV Gp120 CD4 T cells,
- some animal virus undergo latency such as monocytes,
herpesvirus
 Introduction to Virology 6

macrophages, Family Site of Replication

dendritic cell
DNA Adenoviridae Nucleus
Gp41 CCR5; CXCR4 (co- T cells
receptor) (abundantly in Circoviridae
Th1 cells), Hepadnaviridae
Macrophages Herpesviridae
PRRSV GP2a CD163 Monocyte or
and Macrophage Iridoviridae
GP4 Papovarviridae
M-GP5 Heparan Sulfate ECM, Cell Parvoviridae
surface
Asfarviridae Cytoplasm
GP5 Porcine sialic acid Macrophages
receptor (pSn) or e.g. alveolar Poxviridae
Sialoadhesin located in the RNA Bornaviridae Nucleus
upper Orthomyxoviridae
respiratory tract
Retroviridae
Arenaviridae Cytoplasm
2. Penetration Astroviridae
- Penetration is mediated by receptors or entry factors Bunyaviridae
Coronaviridae
Penetration Process Caliciviridae
1. Virus binds with host receptor causing a Filoviridae
conformational change in the viral particle or Paramyxoviridae
attachment protein necessary for cell entry Piconaviridae
2. Cell receptor is immobilized once the viral Rhabdoviridae
particle binds with it. This triggers a cellular Reoviridae
response and internalization of virus-receptor Togaviridae
complex; and
3. Virus-receptor complex induces translocation of 5. Maturation
the complex to an appropriate entry site or to a
site that permits contact with a co-receptor. - Once the virion components are produced, it is
followed by self-assembly and maturation into a stable
and infectious entity
- Virus assemble at the site of replication.
- Maturation may occur as a consequence of specific
cleavage of capsid protein to form mature product.
- This may cause conformational changes in
the capsid or condensation of nucleoproteins with the
genome
3. Uncoating - E.g. HIV matures through proteolytic
- After penetrating, the virion uncoats, liberating its cleavage of Gag (fusion of matrix, capsid, and
nucleic acid. nucleocapside proteins) into matrix,
nucleocapsid, and capsid proteins
- This usually involves exposure of the viral genome,
usually in the form of a nucleoprotein complex 6. Release

4. Replication - After assembly, progeny may stay or exit depending

- Protein and Nucleic acid synthesis vary among
different families of virus
- The liberated nucleic acid is transported to its
replication site (nucleus or cytoplasm)
- Viruses must possess the necessary enzymes for
replication in order to replicate in the cytoplasm
Site of Replication of Animal Viruses
on their type
- For lytic virus (mostly non-enveloped virus), cell
breaks open and release the virus
- Enveloped virus acquire lipid membrane as they bud
out through the cell membrane (no lysis)
Pathogenesis of Viral Infection and Disease
 Introduction to Virology 7

Infection: initial entry of a pathogen to its host, but 4. Virulence;

does not necessarily lead to a disease 5. Patterns of viral infection and disease;
6. Host factors; and
Disease: deviation from a condition which is 7. Host defense
considered normal for a species or type
Virus differ greatly in their virulence. Viruses posses a
Viral Pathogenesis: the process by which viruses
set of genes that code for their virulence, several virus
produce disease in its host
gene contribute to the virulence in some viruses.
For viruses to cause a disease, they must
Determinant of Host Susceptibility and Resistance
1. Escape from the host’s primary physical and
to Viral Infection
natural protective barriers
2. Evade local tissue and immune defenses Host genetic background influences the outcome of a
3. Spread in the body viral infection.
4. Destroy cells either directly or via immune
and inflammatory response - Myxosomavirus causes benign fibroma in wild
rabbits but fatal generalized diseases in European
Viral virulence and host susceptibility are among main rabbits.
factors which contribute to the outcome of virus-host
interaction. - Zoonotic infection are severe in human but milder or
subclinical in their natural reservoir host.
Disease results from favoring transmission of the virus
to that host. - SIV is more pathogenic in humans but not in
chimpanzees and apathogenic in sooty mangabeys
and African green monkeys.
Physiologic Factors that can affect
susceptibility to viral infection
1. Age
2. Sex and levels of certain hormones
3. Nutritional status
4. Parasite load

Epidemiologic triad depicting causal factors of 1. Age

disease
The outcome of viral infection depends on the
interaction of these causal factors.
Responses to viral infection may range from
subclinical illness to full-blown, life-threatening
disease.
Most infections are subclinical and detected only when
serologic or other sensitive assays are used.
Exposure without infection means the absence of cell
entry of the virus.
- viral infection are more serious among very young
and very old
- Faster progression of AIDS, as well as mortality, are
observed in older patients
- Classical Swine Fever Virus are often few mild
clinical and pathological signs among adult animals
- Neonatal pigs are severely affected by Porcine
Epidemic Diarrhea
2. Sex and Level of Certain Hormones

Subclinical or asymptomatic infection implies that viral
multiplication occurs in the absence of viral
maturation.
Key stages of Viral Pathogenesis
1. Transmission and Viral entry to host;
2. Spread in host;
3. Tropism;
- Male and female differ greatly in their response to
viral infection
- Females in general are less susceptible to viral
infection
- stronger immune response resulting to faster
clearance of the virus
 Introduction to Virology 8

- Disease outcome (severity and mortality) can be Antibodies also has an antiviral activity, either
worse for females against free-virus or a virus-infected cell.

- Hormonal milieu plays an important role in Neutralization: is the loss of infectivity as a result
determining the sex-specified responses to viral of binding of an antibody molecule to a viral particle.
infection.
Complement activation, mediated by antibodies, is
- E2 among female suppress the antiviral another antiviral activity towards free virions.
response resulting to reduced immunity during
pregnancy Neutralization by complement activation is lysis of
an enveloped virus or steric hindrance due to
- E2 as well reduces Influenza A virus titer,
buildup of protein molecules.
suggesting an antiviral activity against so
3. Nutritional Status Non-neutralizing antibodies bind to viral proteins
present in virus-infected cells such as nonstructural
- Deficiency in Vitamin E and selenium may result to proteins or altered forms of envelope proteins.
switch from avirulent to virulent Coxsackievirus in mice
4. Parasite Load Viral Strategies to Avoid Host Defense
Mechanism Examples
- Overall microbial environment of a host may alter the Cell to cell spread through - Equine infectious anemia
outcome of a viral infection membrane fusion virus
- Canine distemper virus
- E.g. helminth infection may reactivate viruses such Infection of non- - Herpesviruses in
as herpesvirus. Helminth infection may also impair permissive, resting or ganglionic neurons and B
early stages of HIV infection. undifferentiated cells lymphyocytes
- Papillomaviruses in basal
epithelial cells
Destruction of immune - Infectious bursal disease
Immune Evasive Strategies of Virus effector cells by infection of virus
lymphocytes - Feline panleukopenia
The complex antiviral activity of the host involves a virus
combination of innate and acquired (adaptive) - FIV
immunity. Destruction of immune - Porcine reproductive and
effector cells by infection of respiratory syndrome virus
Virus infection activates several innate immune macrophages - African swine fever virus
receptors (or pattern recognition receptors) which Antigenic drift - Maedi visna virus
causes the production of pro-inflammatory - Equine infectious anemia
cytokines. virus
- Influenza virus
- African swine fever virus
Interferons (IFNs): family of cytokines produced by
No antibody produced - Scrapie
virus-infected cells. Central innate response to viral
infection or the first line of defense against viruses

IFNs signal cells to produce new proteins with

antiviral activity. They also inhibit viral protein
synthesis by preventing translation initiation of
mRNA.

Gamma-IFNs from activated T cells activate

macrophages, which phacoytose virus-infected
cells.

NK cells, like macrophages, kills virus-infected cells,

as well as prime other immune cells.