MCB

VIROLOGY

INTRODUCTION

⁃ Viruses are acellular, obligate intracellular parasites that depend on

host cells for replication.
⁃ They consist of genetic material (DNA or RNA) enclosed in a protein
coat (capsid) and sometimes an envelope.
⁃ Key differences from bacteria, fungi, and parasites:
• No cellular structure (no organelles, cytoplasm, or metabolic
machinery).
• Cannot replicate independently— require host ribosomes, enzymes, and
energy.
• Much smaller (20–300 nm) and only visible via electron microscopy.

HISTORICAL MILESTONES
⁃ 1892: Dmitri Ivanovsky discovered tobacco mosaic virus (TMV)—first
evidence of a non-bacterial infectious agent.
⁃ 1898: Martinus Beijerinck coined the term "virus" (Latin for "poison").
⁃ 1935: Wendell Stanley crystallized TMV, proving viruses are non-living
particles.
⁃ 1949: John Enders grew poliovirus in cell culture, paving the way
for vaccine development.
⁃ 1983: Discovery of HIV (Human Immunodeficiency Virus).
⁃ 2020: Rapid sequencing and vaccine development for SARS-CoV-2 (COVID-19
pandemic).

VIRUS CLASSIFICATION SYSTEMS

⁃ There are various systems but the following are the most pronounced:
• The Classical system: based on hierarchical system.
• The Genomic system: based on DNA/RNA sequencing.
• The Baltimore System: Based on mRNA synthesis mechanism.

UNIQUE PROPERTIES
⁃ Genetic material diversity: DNA (single/double-stranded,
linear/circular) or RNA (positive/negative sense, segmented).
⁃ No metabolic activity outside host cells (cannot generate ATP or
synthesize proteins).
⁃ High mutation rates (especially RNA viruses like HIV and influenza).
⁃ Host specificity (e.g., hepatitis viruses infect liver cells, HIV
targets CD4+ T cells).

STRUCTURE

⁃ Nucleic Acid (Genome);

• DNA viruses (e.g., Herpesviruses, Hepatitis B).
• RNA viruses (e.g., HIV, Influenza, SARS-CoV-2).
• Segmented genomes (e.g., Influenza has 8 RNA segments).

⁃ Capsid (Protein Coat);

• Made of repeating protein subunits (capsomeres).
 • Symmetry of viruses is based on the arrangement of capsomeres.
• Nucleic Acid + Capsid = Nucleocapsid
• Symmetry types:
• Cubic (icosahedral) symmetry:
• The virus particle is icosahedral in shape (almost spherical particle)
and the nucleic acid is contained inside the capsid.
• The icosahedron particle is composed of 20 equilateral triangles, 12
vertices and has 2-3-5 rotational symmetry.
• It is also referred to as polyhedral.
• E.g., Adenovirus, Poliovirus.
• Helical symmetry:
• The virus particle is elongated or pleomorphic (not spherical), and the
nucleic acid is spiral.
• Caposomeres are arranged round the nucleic acid.
• E.g., Rabies virus, TMV.
• Complex symmetry:
• The virus particle does not confirm to either the cubic or helical
symmetry.
• E.g., Poxviruses, Bacteriophages)
• Function:
• Protects nucleic acid from inactivation by the outer physical
conditions.
• Used by naked viruses for moving into the host cell

⁃ Envelope (Lipid Bilayer);

• Derived from host cell membranes during budding.
• Contains viral glycoproteins (e.g., HIV’s gp120, Influenza’s
hemagglutinin).
• Enveloped (e.g., HIV, HSV, Influenza) → More susceptible to
disinfectants.
• Non-enveloped (e.g., Poliovirus, Adenovirus) → More stable in the
environment.
• Function:
• Protect the nucleocapsid
• Used by enveloped viruses for moving into the host cell
• Structure:
• Composed of host membrane lipids and viral encoded proteins
• The host lipid origin could be;
• Cell membrane
• Nuclear membrane
• ER membrane

⁃ Viral Enzymes;
• Reverse transcriptase (Retroviruses like HIV).
• RNA-dependent RNA polymerase (RNA viruses).
• Neuraminidase (Influenza virus).

VIRAL PATHOGENESIS

CHALLENGES VIRUSES FACE

⁃ How to get into the suitable host once it finds it.
⁃ How to replicate during Js time inside the cell.
• Synthesizing mRNA for protein production
• Synthesis of its genetic material
⁃ How to evade the host defenses.
⁃ How to spread from one individual to another.
ROUTES OF ENTRY
⁃ Respiratory (Flu, SARS-CoV-2)
⁃ Blood (HIV, HBV)
⁃ Fecal-oral (Rotavirus, Polio)
⁃ Sexual (HPV, HIV)
⁃ Contact (Ebola, Lassa)
⁃ Others;
• Ocular (Adenovirus)
• Congenital (Zika, CMV)

VIRAL LIFE CYCLE

⁃ Attachment;
• Virus are only able to infect a limited spectrum of cell types (host
range)
• Adsorption occurs primarily by random collision.
• Interaction is between specific proteins on viral surface and specific
receptors on target cell membrane
• However not all cells carrying a receptor for a particular virus can be
productively infected by that virus
• Some viruses may use more than one host cell receptor (e.g. HIV uses
CD4 and two co-receptors (CCR5, CXCR4)
• Most neutralizing antibodies are specific for viral attachment
proteins.

RECEPTOR VIRUS
ICAM-1 Polio
CD4 HIV
Acetylcholine Rabies
EGF Vaccinia
CR2/CD21 Epstein-Barr
HVEM Herpes
Sialic acid Influenza, reo, corona

⁃ Entry;
• Defined as the nucleocapsid penetrating with the animal host cytoplasm.
• There are two basic modes of entry for viruses;
• Fusion:
• Only enveloped viruses can use this means
• It involves the virus leaving behind its envelope in the cell membrane
of its host.
• E.g. HIV, Herpes virus
• Endocytosis:
• It involves using the regular cellular feeding mechanism
• All non-enveloped viruses use this means
• E.g. Polio virus, Toga virus
• Both modes of entry are receptor mediated and result in the formation
of a ‘phagolysosome’ in the endocytosis-mediated mechanism
• Some enveloped viruses use fusion as means of entry. Eg., Hepatitis C
virus
• A third means of entry is ‘genetic injection’ which primarily seen in
viruses that infect bacteria i.e. bacteriophages. It involves inserting only the
nucleic acid into the cytoplasm of its host.

⁃ Uncoating;
• Defined as release of viral genome into the host cytoplasm from the
nucleocapsid.
 • Host cellular enzymes (lysosomes) strip off the virus protein coat.
• Thus once uncoating happens the host ability to sense the virus is
severely diminished.
• At this stage the patient is infected but the virus cannot be detected.
This is called the ‘eclipse phase’.
• The length of the eclipse phase is very dependent on the specific viral
agent.

⁃ Replication;
• Defined as the synthesis of viral progeny ‘genome and protein’ from the
parent viral genome.
• It is dependent on the nucleic acid composition of the virus.
• It is the basis for the Baltimore Classification system.
• The ‘site’ and ‘manner’ of replication are very important
• Site:
• All DNA viruses replicate in the nucleus (except Pox virus)
• All RNA viruses replicate in the cytoplasm (except Influenza virus)
• Manner:
• Dependent on the genome composition

⁃ Assembly;
• Defined as the formation of the ‘nucleocapsid’.
• New viral genomes and proteins are put together to form potential viral
particles.
• Site of assembly is directly related to the site of genome replication.
• Nucleus for DNA viruses except for Poxvirus which replicates in the
cytoplasm.
• Cytoplasm for RNA viruses except for Influenza virus which replicates
in the nucleus.

⁃ Release;
• Defined as exit of the mature viral particle from the host cell.
• Enveloped viruses:
• Released by budding from the infected cells thus leaving the host cell
intact.
• However some enveloped viruses might become lytic during disease.
• Example is Herpesviruses which is usually latent but could become lytic
during symptomatic phases.
• Naked viruses:
• Released by rupture/lysis of the infected cells thus killing the host
cell.
• Viruses might be lytic in some cell types while in other cell types it
could be released by exocytosis.

REPLICATION IN DNA VIRUSES

⁃ Double-stranded DNA (dsDNA);

• After uncoating in the cytoplasm the viral DNA moves into the nucleus.
• The virus then replicates its DNA in the host cell nucleus mediated by
cellular and/or viral DNA polymerase.
• Those that rely on host cellular enzymes have a slower replication
cyclE.
• The synthesis of capsid and other proteins are in the cytoplasm using
host cell enzymes.
 • New viral proteins move to nucleus where they combine with new DNA.
• Note that some dsDNA might become latent once inside the host nucleus,
which means that the viral genome is present but not replicating in the host cell.
• Latency is associated with DNA viruses but not to RNA viruses.
• Examples:
• Herpesvirus:
• Latency (e.g., HSV in neurons; genome circularizes).
• Uses viral DNA polymerase (target for antivirals, e.g., Acyclovir).
• Hepadnavirus:
• Reverse transcription step (HBV pre-genomic RNA → DNA via reverse
transcriptase).
• Poxviruses:
• Replicates in cytoplasm (carries own DNA/RNA polymerases).

⁃ Single-stranded DNA (ssDNA);

• The single copy must first be polymerizzed to its complementary strand
to form a double stranded virus in the nucleus.
• Thus an ‘intermediate dsDNA’ is needed before replication can continue.
• Replication then continues as for dsDNA.
• Examples:
• Parvovirus

REPLICATION IN RNA VIRUSES

⁃ Single-stranded sense RNA (ss[+]RNA);

• The viral RNA is first directly translated to make early proteins.
• Importantly among the early protein is RNA-Dependent RNA Polymerase
(RDRP) production.
• Synthesis of (-)sense RNA is then made from the original (+)sense
template using the RDRP.
• The combination of the three leads to the formation of the ‘replicative
complex’ (RC)
• This causes synthesis of (+)sense RNA and (-)sense RNA copies.
• The new (+)sense RNA (i.e. mRNA) copies are translated to viral protein
while the new (-)sense RNA copies are used to make more (+)sense RNA i.e. for
future viral genome.
• (+) RNA viral genome is capable of completing a successful replication
cycle once inside the cell ( i.e. without the capsid) but not the (-) RNA viral
genome.
• Examples:
• Picornaviridae
• Caliciviridae
• Astroviridae
• Coronaviridae
• Flaviviradae
• Togaviridae

[ NOTE: RDRP also known as “transcriptase” is not contained in the structure of the
(+) ssRNA. It does not need the ready made enzyme as (+) ssRNA can be translated
like an mRNA. ]

⁃ Single-stranded antisense RNA (ss[-]RNA);

• The (-)ssRNA is non-coding (antisense) and cannot be directly
translated by host ribosomes because the mammalian genome does not code for RDRP.
• The (-)sense RNA must first be used to make complementary (+)sense RNA
copies with the RDRP carried into the host by the infecting virus.
 • The new (+)sense RNA made from the original (-)sense template and the
RDRP make the ‘replicative complex’ (RC).
• This leads to synthesis of (+)sense RNA and (-)sense RNA copies.
• The (+)sense RNA (i.e. mRNA) copies are translated to viral protein and
also to make (-)sense RNA copies for future viral genome.
• Examples:
• Orthomyxoviridae
• Paramyxoviridae
• Rhabdoviridae
• Filoviridae

⁃ Double-stranded RNA (dsRNA);

• It doesn’t use the (+) strand of viral genome directly as a mRNA as it
can not be used.
• It proceeds like a (-) sense RNA virus except that its final structure
contains both complements of the viral genome.
• Thus it also comes into the host cell with its RDRP.
• It is different from a DNA virus in that it is not dependent on host
cellular polymerase activity.
• Example:
• Reoviridae

REPLICATION IN OTHER VIRUSES

⁃ Retroviruses;
• (+)ssRNA with reverse transcriptase (RT)
• RT is used to make a DNA copy using the viral RNA as a template.
• The Single DNA is then used as a template to make a complementary copy
thus making it double.
• The dsDNA of the virus is then integrated into the host genome by
‘integrase’ (latency).
• Genomic integration is an ability of retroviruses only.
• Example:
• HIV

⁃ Hepatitis B virus;
• dsDNA with reverse transcriptase (RT)
• The genome which is described as “gapped dsDNA” or “partially dsDNA” is
completed by a viral DNA polymerase.
• RT is not used to complete the “incomplete genome” of the virus but to
make Viral DNA from mRNA in the cytoplasm.

DNA VS. RNA VIRUS REPLICATION

FEATURE DNA VIRUS RNA VIRUS

Polymerase Host/viral DNA pol Viral RDRP (error-prone)
Replication site Nucleus (mostly0 Cytoplasm
Mutation rate Low High
Example drug Acyclovir (HSV) Remdesivir (SARS-CoV-2)

IMMUNE RESPONSE TO VIRAL INFECTION

⁃ Innate Immune Response;

• Physical & Chemical Barriers:
 • Skin and mucosal membranes block entry.
• Mucus, saliva, tears contain antiviral enzymes (e.g., lysozyme,
lactoferrin).
• pH of the stomach inactivates many viruses.

• Pattern Recognition Receptors (PRRs):

• Detect Pathogen-Associated Molecular Patterns (PAMPs):
• dsRNA
• ssRNA
• DN
• Key receptors:
• Endosomes: TLR3, TLR7, TLR9
• Cytosol: RIG-I, MDA5
• Trigger production of:
• Type I Interferons (IFN-α and IFN-β)

• Type I Interferons (IFNs):

• Induce antiviral state in neighboring cells.
• Upregulate MHC I, activating cytotoxic T lymphocytes (CTLs).
• Inhibit viral replication by:
• Protein kinase R (PKR): blocks translation.
• RNase L: degrades viral RNA.

• Natural Killer (NK) Cells:

• Detect downregulated MHC I on infected cells.
• Kill via perforin and granzymes.
• Produce IFN-γ to activate macrophages and promote Th1 response.

• Complement System:
• Activated via classical or alternative pathways.
• Lyses enveloped viruses.
• Enhances opsonization and phagocytosis.

⁃ Adaptive Immune Response;

• Humoral Immunity (B cells):

• Naïve B cells recognize viral antigens via surface IgM.
• Due to influence of CD4+ Th cells, undergo class switching to produce:
• IgG
• IgA
• IgM
• Functions:
• Neutralization: block virus attachment/entry (IgA)
• Opsonization: enhance phagocytosis.
• Antibody-dependent cell-mediated cytotoxicity (ADCC): via NK cells.
• Complement activation.

• Cell-Mediated Immunity (T cells):

• CD8+ Cytotoxic T Lymphocytes (CTLs)
• Recognize viral peptides on MHC I.
• Kill infected cells by:
• Perforin/granzyme pathway
• Fas-FasL interaction
• Essential for clearing intracellular viruses.

• CD4+ Helper T Cells

• Recognize viral peptides on MHC II from APCs.
• Differentiate into:
 • Th1 cells: secrete IFN-γ, activate macrophages, support CTL responses.
• Th2 cells: help B cell antibody production.
• Tfh cells: support germinal center formation and high-affinity antibody
production.

IMMUNE EVASION BY VIRUSES

⁃ Host tropism;
• Viruses infect specific tissues based on receptor compatibility.
• Examples:
• HIV → CD4+ T cells (binds CD4 + CCR5/CXCR4)
• Influenza → Respiratory epithelium (binds sialic acid)

⁃ Immune Evasion Strategies;

• Viruses encode proteins that interfere with the various levels of
specific and nonspecific host defenses.
• Examples:
• Antigenic Variation (e.g., Flu shifts/drifts, HIV mutations)
• Latency (e.g., HSV hides in neurons, Varicella-Zoster reactivates as
shingles)
• Blocking actions of IFN-α & IFN-β (e.g., Hepatitis C degrades IFN
pathways)
• MHC Downregulation (e.g., CMV prevents antigen presentation)

ONCOGENIC VIRUSES
⁃ 20% of human cancers are believed to be of viral origin.
⁃ Although both RNA and DNA viruses are implicated, DNA viruses are more
so because of their ability to interfere with the cell cycle as important means of
their survival.
⁃ Retroviruses are the most implicated family the RNA virus class.
⁃ There is no single mechanism by which viruses cause cancer.
⁃ Viruses are not the only factor as host factors are more important.

CANCER VIRUS
Cervical cancer HPV
Burkitt’s lymphoma EBV
Hepatocellular carcinoma HBV; HCV
Kaposi’s sarcoma KSHV
Adult T cell lymphoma HTLV