University of Balamand

Faculty of Medicine and

Medical Sciences

CVIR401
Lecture#1 (Part#2)
Viral Biology and Pathogenesis

Instructor: Samer Bazzi, PhD

How can viruses affect host cells?
- Viruses may inhibit host cell DNA, RNA or/and protein synthesis by various
mechanisms

- Viruses can regulate cellular gene expression to increase virus ability to grow or to
diminish defense mechanisms

- Viral presence often gives rise to morphological changes in host cells. Any
detectable change in host cell due to infection is called cytopathic effect (CPE) Not
all viruses cause CPEs

- Certain viruses induce, delay or suppress apoptosis in infected cells:

Apoptosis  leads to cell destruction and therefore to diminished effector function

(e.g. HIV and CD4 cells)

Apoptosis may also be a host defense mechanism cells die before virus completes
its replication cycle  limit spread

 Viruses causing acute infections can delay cell apoptosis long enough to produce
progeny virions

 Persistent viruses suppress apoptosis for longer time to maintain a compartment of

infected cells
Cytopathic Effects (CPEs)
 CPE is applied to virus-induced cellular changes that are usually visible by
light microscopy

Cell Formation of Death

rounding multinucleated
Swelling or giant cells
shrinking (Syncytia)
Production of
Cell
intracellular
disorientation
Detachment masses (inclusion
from surface bodies) in nucleus
or cytoplasm

CPE-related cellular changes can be detected by staining with chromatic dyes

 basic (haematoxylin) and acidic (eosin) dyes
 Selected Types of Cytopathic Effects (CPEs)

Adenovirus infection leading Measles virus infection leading to

to inclusion bodies Syncytia

- Enveloped viruses with fusion proteins

 infected cells become
rounded
 dark basophilic inclusions
within nuclei represent
accumulated viral proteins at
- Multiple nuclei are clustered around an
the site of virus assembly
expressed at the cell membrane can
result in fusion of neighboring cells 
formation of multinucleated cells or
syncytia
eosinophilic cytoplasmic mass probably
representing Golgi compartments of
fused cells
 Nature of Viral Infections In Relation to Host Cells

- Abortive/Non-Permissive: there is no viral replication, so no virion progeny are formed

and there is no established latency

- Productive/Lytic: cells are permissive for viral replication and virion progeny release.
This can lead to lysis of cells (lytic infection)

- Persistent/Productive: cells are permissive for viral replication and virion progeny
release; however, there is no cell death (cellular senescence)

- Persistent/Latent: cells are transiently/semi permissive for viral replication and few virus
particles are produced. Virus production then ceases but the genome persists.

- Persistent/Transforming: Oncogenic transformation may then develop due to selective

expression of viral genes encoding proteins that interfere with the cell cycle of host cells
leading to their uncontrolled growth
Viral Pathogenesis
- Process by which a viral infection can lead to disease can be
mediated by cell destruction, by virus-induced changes in cellular
gene expression, or/and by immune-based mechanisms.

- There are 8 critical viral pathogenesis stages that determine the

nature of disease:

Viral Pathogenesis Stage 1: Entry into the host

- Site of entry may influence disease symptoms
- Infection can occur via:
Skin: virus entry requires a breach in the physical integrity of this
effective barrier (cuts or abrasions). Viruses can employ arthropod
vectors (ticks, mosquitoes) or animals (bites) to breach this barrier.

Respiratory tract: viruses must overcome sophisticated immune

defense mechanisms at all mucosal surfaces as well as non-
specific inhibitory mechanisms (cilia, mucus, etc.)

Gastrointestinal tract: a hostile environment due to gastric acid

Genito-urinary tract: less hostile but less frequently exposed

Conjunctiva: exposed site and relatively unprotected; easy infection

Blood: direct inoculation by transfusion, by needle injection, or by

arthropod vectors
Viral Pathogenesis Stage 1: Entry into the host
Modes of Virus Transmission

- Airborne transmission: via aerosols through coughing/sneezing. Example: Influenza A

virus, Rhinoviruses, SARS-CoV2

- Fecal-oral transmission: ingestion of viruses leads to high level replication in the gut.
Example: Enteroviruses and Rotaviruses.

- Blood-borne transmission: viruses are transferred through contaminated blood products

and sharing of contaminated needles. Example: Hepatitis B virus or HIV

- Sexual Transmission. Example: HIV or HSV-2.

- Vertical transmission: transplacental, during delivery, and through breast feeding

(Cytomegalovirus)

- Animal or insect vectors: some viruses are generally transmitted to humans by direct
inoculation. Example: Rabies virus or Dengue virus.

- Skin contact: HSV or Poxviruses

Viral Pathogenesis Stage 2: Replication Site
- Following entry into a host, viruses must initiate infection by invading and replicating in
susceptible cells. This determines whether the infection will be localized or systemic.

Localized Infections
Virus Primary Replication
Rhinoviruses Upper Respiratory Tract
Rotaviruses Intestinal epithelium
Papillomaviruses Epidermis

Systemic Infections
Virus Primary Replication Secondary Replication
Enteroviruses Intestinal epithelium Lymphoid tissues, CNS
Herpesviruses Oropharynx or G.U. tract Lymphoid cells, CNS
Viral Pathogenesis Stage 3: Spread Throughout the Host

- Apart from direct cell-cell contact, there are two

main mechanisms for virus spread/dissemination
throughout the host:
→ via the bloodstream
- The virus may travel free in the plasma
(Togaviruses, Enteroviruses), or associated with
RBCs (Orbiviruses), platelets (HSV), lymphocytes
(EBV, CMV) or monocytes (Lentiviruses)
- When virus reaches the blood, a primary low
viremia usually occurs, followed by generalized
higher titer secondary viremia as the virus reaches
and replicates in other target tissues.
→ via the nervous system
- Spread to nervous system can occur either
directly, by contact with neurons at the primary site
of infection, or via the bloodstream
- Once in peripheral nerves, the virus can spread to
the CNS by axonal transport along neurons (classic
– HSV). Viruses can cross synaptic junctions since
these frequently contain virus receptors, allowing
the virus to jump from one cell to another.
Viral Pathogenesis Stage 4: Cell/Tissue Tropism
- The ability of a virus to replicate in particular cells
or tissues is controlled by:
→ route of infection
→ interaction of virus attachment protein with
specific receptors on cell surface
→ cellular factors supporting virus replication

Viral Pathogenesis Stage 5: Host Immune Response

- Has a major impact on the outcome of infection
Viral Pathogenesis Stage 6: Secondary Replication
- In systemic infections, virus reaches other tissues and is capable of replicating in these
tissues. For example:
• Poliovirus: gut epithelium → neurons in brain and spinal cord
• Lentiviruses: macrophages/T cells → CNS + other tissues
- If viruses could be prevented from reaching tissues where secondary replication occurs,
generally no disease will be produced
Viral Pathogenesis Stage 7: Cell/Tissue Damage
- Generally, disease occurs when viral replication leads to cell damage or cell death.
- Many retroviruses cause persistent infection without cell death or disease and retrovirus
genomes have been in humans for thousands of years
- In contrast, Rhinoviruses cause lysis of cells leading to fever and increased mucus
secretions whereas Poliovirus can damage anterior horn motor neurons and lead to
paralysis or death.

Viral Pathogenesis Stage 8: Persistence Versus Clearance

- The outcome of any virus infection depends on the balance between these 2 processes
- Acute viral infections are commonly cleared (eliminated) by the immune system (for
example Rhinoviruses)
- Other viruses can cause persistent/latent infections with major tissue damage (for example
HIV and Herpes viruses).
Persistence of a viral infection results from two main mechanisms:
- Regulation of lytic potential to produce a critical number of virus-infected cells
without killing the host
- Evasion of immune surveillance which might occur because of:
A- Antigenic variation:
i- Antigenic drift with gradual accumulation of minor mutations in viral
genome  altered antigenicity  decreased recognition by the
immune system
ii- Antigenic shift: major rapid and drastic change in antigenicity due to
recombination between a virus genome with the genome of another virus
from a different antigenic type  failure of immune system to recognize new
antigens (i.e. influenza virus)
B- Immune tolerance (genetic factors, molecular mimicry)
C- Restricted cellular gene expression (i.e. MHC-I expression)
D- Infection of immunocompromised sites (i.e HSV in sensory ganglia of the CNS)
E- Direct infection of immune cells resulting in immunosuppression (HIV,
Herpesviruses)
Stages of Viral Infection Development
The process of viral infection is categorized into different stages:
1- Incubation: period between the first exposure to a virus and the first emergence of symptoms
(infected person does not show any signs or symptoms of sickness and may or may not transmit the
virus).

2- Prodromal: an intermediate period between incubation and illness (infected person can transmit the
virus). General and non-specific signs and symptoms of illness appear (i.e. fatigue)

3- Clinical disease (illness): this stage includes the time when an infected person shows infection-
specific signs and symptoms

4- Decline: the immune system mounts a successful defense against the virus and the number of
infectious viral particles decreases. Symptoms will gradually improve.

5- Convalescence: recovery from

infection. Symptoms start to disappear
until a person is fully healed.
Patterns and Time Courses of Viral Infection/Disease
Acute infection Virus titer
- Virus actively replicating Disease state
- Symptoms progressing
- Effective immune responses would lead to virus Rhinovirus
clearance and complete remission in most cases Time (days)

Acute infection with rare late complication

- Example: subacute sclerosing panencephalitis No intact virus is made
(SSPE) that can follow an acute measles
infection
Time (days) Time (years)

Some viral
Latent infection proteins are
- Example: varicella-zoster virus (VZV) synthesized to
maintain latency

VZV (Chickenpox) VZV (Shingles)

Time (days) Time (years) Time (days)

Chronic infection Viral shedding

- Example: chronic Hepatitis B

Hepatitis B
Time (months) Time (years)
Patterns and Time Courses of Viral Infections
Chronic infection with late disease onset

HTLV-1 or HIV
Time (years)

Slow infection
- A prolonged incubation period, lasting
months or years, during which virus
continues to multiply. Clinical symptoms are
usually not evident during the long incubation JCV
period (Example: JCV)
Time (years)
Genetic and Non-Genetic Mechanisms Leading to Variations of Viruses
Mutations
Example: point mutations, insertions, deletions
Recombination
Recombination occurs when at least two viral genomes
(segmented or non-segmented) co-infect the same host
cell and exchange genetic fragments of their genome

Reassortment
Viruses with segmented genomes exchange genetic
material (i.e. antigenic shift)

Complementation
Virus A Virus B
- When 1 of 2 viruses that infect the cell has a mutation that
results in a nonfunctional protein.
- The non-mutated virus “complements” the mutated one by
making a functional protein that serves both viruses.

Phenotypic mixing
- Occurs with simultaneous infection of a
cell with 2 viruses
- For progeny 1, genome of virus A can be
partially or completely coated (forming pseudovirion)
with the surface proteins of virus B.
- Type B protein coat determines the tropism (infectivity) of the hybrid virus.
- Progeny from subsequent infection of a cell by progeny 1 will have a type A coat that is encoded
by its type A genetic material.
 Immune defenses against viruses
• Physical barriers and phagocytosis
• Non-specific responses (in hours) including
fever, inflammation, NK cells, interferons and
non-specific inhibitors of virus infection
• Immune responses through adaptive
immunity (in days)
Role of macrophages
• Phagocytosis with or without opsonization;
antigen presentation; ADCC; cytokine
release (IL-12→Th1); interferon production
→ direct inhibition of viral replication and
promoting Tc and NK cell functions
Role of humoral response
• Antibody responses (in days)→ ADCC,
neutralizing antibody, and lysis of infected
cells by antibody + complement. Maternal
Abs protect neonate.
Role of cellular responses
• Tc cells → kill infected cells; Th cells →
MHC-II-driven responses; NK cells→ kill
infected cells by recognizing changes on the
surface of infected cells or by ADCC
Effective Sterilization and Disinfection Methods Against Viruses

- Enveloped viruses, are generally labile and do not survive well outside host cells

- Unlike naked viruses, enveloped viruses are inactivated by heat, detergents, acid and
organic solvents like ether and alcohols

- Some viruses (HBV) are resistant to inactivation. Special precautions need to be taken
to avoid transmission among healthcare workers.

- Moist heat (autoclaving 120°C for 20min) or dry heat (oven 180°C for 60min) are
effective against all viruses

- Chemicals: halogens especially chlorine as hypochlorite are effective against viruses

but corrosive on instruments → use activated glutaraldehyde « Cidex »

- Detergents and lipid solvents: inactivate enveloped viruses which need intact envelope
for adsorption → phenolic disinfectants damage viral proteins but do not affect nucleic
acids. Therefore not recommended for viral disinfection.
Figures and Graphs Used in this Presentation were taken from:

- Le, Tao; Bhushan, Vikas; and Sochat, Matthew. First Aid for the USMLE Step 1 2021.
New York: McGraw-Hill Education, 2021.

- https://www.sciencedirect.com/

- https://www.researchgate.net/