VIRUSES: CLASSIFICATION,

GENERAL CHARACTERISTICS,
REPLICATION

MICHAEL BALDWIN PH.D.

FALL SEMESTER 2018
 LEARNING
OBJECTIVES
• Define the nature of a virus and explain how a virus
differs from a cell

• Describe the major classes of viral genomes and cite

an example of each

• Describe the replication cycles of viruses

• Describe mechanisms of viral pathogenesis

 WHAT ARE VIRUSES?
• Viruses are generally considered non-living entities
• Highly adapted intracellular parasites?

• Viruses cannot generate energy or produce proteins

independent of a host cell

• Viruses do not have the genetic capability to multiply

by division

• Viral genome can be RNA or DNA, but not both

• Viruses have a naked capsid or envelope with attached

proteins
WHAT ARE VIRUSES?
Comparative size of viral agents
 WHAT ARE VIRUSES?
TERMINOLOGY

• VIRION: The infectious particle consisting of the

envelope (some viruses), capsid and the interior core
(genome +/- accessory viral proteins)

• CAPSID: The outer protein shell that protects the interior

core containing the genome and other proteins

• GENOME: genetic material of the virus, either DNA or

RNA

• NUCLEOCAPSID: Capsid + genome

 THE VIRION

Lipid Envelope Nucleic Acid

Protein
Capsid

Virion
Associated
Spike
Polymerase
Projections
 WHAT ARE VIRUSES?
• Like all infectious agents, viruses need to
spread and infect new hosts
• High rates of replication are often very damaging to the
host tissues which can kill the host (reduces
transmission in the long-term)

• High rates of replication are more likely to stimulate an

immune response (reduces transmission)

• Genome/ virion stability within host cells can increase the

likelihood of transmission (increases transmission)
 WHAT ARE VIRUSES?
Examples of viral strategies:
• “Hit and run” (Smallpox)
• Viral production very high
• Exposure relatively short
• Large number of virions increases likelihood of transmission
(short-term)

• “Slow and low” (Hepatitis C virus)

• Viral production very low
• Exposure relatively long
• Immune evasion strategy

• Latency with occasional reemergence

(Herpes simplex virus)
• Viral production is moderate
• Exposure is life long – viral genome integration
• Transmission is relatively targeted
 WHAT ARE VIRUSES?
• Each type of virus infects a particular subset of
species, known as the host range
• Host range is often determined by the ability of the virion
to attach to specific host cell surface receptors  e.g.
Polio virus binds specifically to human CD155
• Host cell machinery is also important in determining host
range  the host cell must be able to successfully
synthesize new virions

• The range of tissue types that a virus can infect

is referred to as the tissue tropism
VIRAL STRUCTURE
• Viral genomes can be composed of either DNA
or RNA, and can be either single stranded (ss) or
double stranded (ds)

• The protein coat that covers the genome is

termed the capsid

• Some viruses such as HIV possess an envelope

layer derived from host membranes that are
decorated with viral glycoproteins (host cell
attachment)
VIRAL STRUCTURE:
FIVE BASIC TYPES
Icosahedral nucleocapsid nucleocapsid

lipid bilayer

ICOSAHEDRAL ENVELOPED ICOSAHEDRAL

helical nucleocapsid

COMPLEX

nucleocapsid

lipid bilayer

glycoprotein spikes (peplomers)

HELICAL ENVELOPED HELICAL

 VIRAL STRUCTURE:
CAPSIDS
Icosahedral capsids:
• Radial symmetry; based on an
icosahedron, a polyhedron with
20 identical triangular faces
• Example: herpes simplex virus
(HSV)
 VIRAL STRUCTURE:
CAPSIDS
Filamentous capsids:
• Helical symmetry; a helical tube
around the genome, which is
wound helically within the tube
• The length may extend to 50
times its width, generating a
flexible filament

• Examples: tobacco mosaic

virus; Ebola virus
VIRAL STRUCTURE: CAPSIDS
Bullet shaped
Rabies virus

Pleomorphic
Ebola virus

Amorphous
Pox viruses

Overall, virion shape and the presence/absence of an

envelope tell us little about host range/disease manifestations
 still useful means to begin viral classification
 VIRAL GENOMES
• Avian Leukosis Virus (ALV) is a small RNA retrovirus
containing only 3 genes  gag, pol, & env

• The 3 genes encode polypeptides that are eventually

cleaved to form a total of 9 functional products

LTR= long terminal repeat; blue section indicates noncoding RNA

 VIRAL GENOMES
• The genomes of some DNA viruses approach or exceed
those of cellular organisms
• Pandoravirus salinus is the largest known virus to date
(2.47 Mbp, 2556 genes)

Pandoravirus salinus infecting an

ameoba
 VIRAL EVOLUTION
• Viruses evolve through genome change and natural
selection  rate of change is 10-100× that of host

• Rapid mutation and evolution of a virus leads to

antigenic drift – virions no longer recognized by
neutralizing antibodies

• Antigenic drift generates new strains of virus that can

cause serious disease
• Classic example is Influenza virus
 VIRAL EVOLUTION
• Over an extended time period, viral evolution generates
new kinds of viruses that cause different diseases in
different hosts
Phylogeny of human and animal
herpes viruses

Whole-genome sequence analysis comparing groups of genes

with similar function. Numbers measure genetic divergence
 VIRAL EVOLUTION
In general, viruses evolve at different levels:
• within a host community – evolve to preferentially infect
different host species

• within a viral species population – strains evolve that vary

in infectivity and virulence (HHV1 and HSV2 cause similar
diseases; HHV3 and HHV5 cause distinct diseases)

• within an individual host organism – viruses evolve

variants that resist therapeutic agents (Hepatitis C and
HIV)
 VIRAL CLASSIFICATION:
THE BALTIMORE MODEL
The Baltimore model distinguishes classes of viruses
based on the following criteria:
• Genome composition (DNA or RNA)
• Whether it is single- or double-stranded
• If single-stranded, whether the strand encodes protein
or requires synthesis of a complement that encodes
proteins

There are 7 Baltimore groups of viruses based on genome

type and mRNA generation.
 THE BALTIMORE MODEL
Human Herpes virus

Parvovirus
Hepatitis B virus

HIV

Polio virus

Rotavirus
Influenza

KNOW THE 7 GROUPS AND MAJOR CHARACTERISTIC, i.e. GROUP I: dsDNA

 VIRAL REPLICATION
• Depends on host organelles and enzymes to produce
new virions

• Replication cycle usually results in death and lysis of

host cell  lytic replication

• Stages of lytic replication cycle:

• Attachment & Entry
• Synthesis & Assembly
• Exit and transmission
VIRAL ATTACHMENT
Viral attachment is dependent on receptors
expressed on the host cell surface
• Proteins

• Carbohydrates
• Glycoproteins
• Glycolipids

Receptor recognition is a major factor in

determining host range and tissue tropism
VIRAL RECEPTORS
You do not need to memorize the table

VIRUS RECEPTOR(S)
Adenovirus CAR
Coxsackievirus CAR, CD55
Echovirus Integrin VLA-2, CD55
Epstein-Barr Virus CD21
HIV-1 CD4, CCR5, CXCR4
Measles virus CD46
Parvovirus Transferrin receptor type 1
Poliovirus CD155
Rhinovirus ICAM-1
 ENTRY AND UNCOATING
• Viral replication requires release of the genome from the
capsid  individual viruses exploit unique strategies

Direct Penetration
The viral capsid or genome is
translocated directly into cytoplasm

Membrane Fusion
Viral envelope fuses with the PM
releasing the nucleocapsid into the
cytoplasm  capsid breaks down
 ENTRY AND UNCOATING
• Viral replication requires release of the genome from the
capsid  individual viruses exploit unique strategies

Endocytosis
• Virion-receptor complex is endocytosed
into cytoplasm

• Viral envelope fuses with the

endosomal membrane releasing the
nucleocapsid  capsid breaks down to
release genome
 SYNTHESIS AND
ASSEMBLY
• Each type of virus requires a different strategy
depending on its nucleic acid
• DNA viruses typically enter the nucleus as they
require the host cell’s DNA-dependent RNA
polymerase
• Smallpox replicates in cytoplasm  encodes its own DNA-
dependent RNA polymerase
• RNA viruses typically replicate in the cytoplasm
• Must consider:
• How mRNA is synthesized? Capped?
• What serves as template for nucleic acid replication?
 SYNTHESIS AND
ASSEMBLY
Genome mRNA synthesis Genome replication Example
dsDNA Host RNA polymerase (in nucleus or Each strand of DNA serves as a Herpes
cytoplasm) template for its complement simplex virus
(exception is HBV)
ssDNA Host RNA polymerase (in nucleus) Complementary strand of DNA is Parvovirus
synthesized to act as template B19
(+) ssRNA Genome acts directly as mRNA (-) ssRNA is synthesized to act as Hepatitis C
template virus
(+) ssRNA DNA is synthesized from viral RNA by DNA HIV
(retroviridae) reverse transcriptase; mRNA is
transcribed from DNA by host RNA
polymerase
(-) ssRNA RNA-dependent RNA polymerase (+) RNA (mRNA) Poliovirus

dsRNA Positive strand of genome acts as Each strand of RNA serves as a Rotavirus
RNA template for its complement
HUMAN PAPILLOMAVIRUS
(HPV): DNA GENOME
• HPV gains access to the actively
dividing cells of the epidermis basal
layer

• Virions are endocytosed by the basal

cells, but replication is inhibited until
basal cells start to differentiate into
keratinocytes

• As the epithelial layers slough off,

progeny virions are shed

• In some infected cells, HPV virions

become latent, persisting for months
or years

• The latent viral genomes may induce

the host cells to form abnormal
growths, such as warts or cancers
INFLUENZA A VIRUS:
NEGATIVE SENSE RNA GENOME
INFLUENZA A VIRUS:
RNA GENOME
RELEASE OF ENVELOPED
VIRUSES BY BUDDING
VIRAL PATHOGENESIS

Viral pathogenesis in general derives from:

• Latency

• Cell death/damage

• Immune-mediated damage
 VIRAL PATHOGENESIS:
LATENCY
• Although many viruses are capable of subclinical
infection, only a few are known to undergo true latency
• Properties of true latency are:
• Maintenance – maintenance of the entire viral genome
within the host cell (nuclear or cytoplasmic retention), but
its expression is dramatically restricted to a few proteins
(no mature virions are produced)
• Persistence – evasion of the hosts immunologic
surveillance system
• Reversibility – i.e., the capacity of the genome to
reactivate full viral gene expression, with production of
infectious virions
 VIRAL PATHOGENESIS:
LATENCY
Latency can be divided into two groups:
• Episomal latency
• Episomal latency refers to the use of episomes during
latency (extra-chromosomal genetic material that may
replicate autonomously)  Herpes viruses

• Proviral latency occurs when the viral genome is

integrated into the host chromosome(s)  retroviruses
such as HIV-1

Latency represents a major barrier to viral

eradication
 VIRAL PATHOGENESIS:
CYTOPATHIC EFFECTS
• Cell death
• Can be virally-induced lysis (Adenovirus) or cellular
apoptosis (Poliovirus)

• Cell fusion
• Certain viruses promote cell-cell fusion to generate,
giant multinucleated cells (HIV, RSV)

• Malignant transformation
• Certain viral infections can lead to cellular transformation
 cancer development
VIRAL PATHOGENESIS: IMMUNE
MEDIATED INJURY
• Cytotoxic T cells
• HAV and HBV both stimulate production of CTLs
which kill infected hepatocytes  accounts for
majority of damage to the liver

• Immune complex deposition

• HBV-antibody complexes can become deposited on
capillary membranes  immune mediated vasculitis
 DIAGNOSIS: VIRAL CULTURE
• Viral culture is useful for both identification and
research into the viral life-cycle
• Culturing of viruses necessarily involves co-culture of
host cells
• Infection often utilizes immortalized cell lines that can be
cultured in perpetuity
• Cells grow rapidly and are effectively clonal
• Cells can be genetically manipulated to identify essential host genes
• Good cellular models are not available for all viruses
• Hepatocytes  HAV, HBV, HCV
• Neurons  Poliovirus, Herpes viruses (latency)
 DIAGNOSIS: PLAQUE ASSAY

Plaque assays can be used to estimate the number of

infectious particles (plaque-forming units, pfu) in a sample
DIAGNOSIS

• Electron Microscopy (direct observation of virions) 

time-consuming, relatively expensive

• Serology (detection of serum antibodies to virus;

indirect method)  inexpensive, relatively insensitive

• Polymerase chain reaction (PCR, direct detection of

viral genomic material)  high sensitivity, can detect
both DNA and RNA viruses, can multiplex, i.e., screen
for multiple pathogens in a single sample.