Viruses and Prions

Professor Leo Poon

School of Public Health
[email protected]

Smallpox (天花)
Learning objectives

What diseases do viruses cause ?

What is a virus?
How does a virus differ from a bacterium?

Practicals
How do viruses replicate and cause disease
How do you grow a virus in the laboratory?
How do you diagnose virus infections?
Other types of agents
 What diseases do viruses cause?
Polio (小兒麻痹症)

Smallpox (天花)
What diseases do
viruses cause?
 What diseases do
viruses cause?
Zika virus: a mosquito transmitted virus

COVID-19 Zika microcephaly

 In a few weeks, the 2009 H1N1v pandemic spread around the
world affecting all countries
* Reports up to July 2009

April 2009

May 2009

First detected June 2009

April 2009 July 6 2009

Cumulative cases
1–10
11–50
51–500

500–5000

>5000

US, Mexico, Canada, UK, Chile and Australia account for ~76% of total cases

WHO, 2009. Pandemic (H1N1) 2009, situation update,

available at: http://www.who.int/csr/don/2009_07_06/en/index.html (accessed 6 July 2009)
COVID-19: >36 million confirmed cases in less than 10 months
Influenza Influenza
What is a virus?

 Human - meters Naked eye

 Human hair - millimeters
 Red blood cell - 7 micrometers Light Microscope
 Candida (yeast) - 5 micrometers
 Escherichia coli - 1-3 micrometers
 Herpesvirus - 0.2 micrometers Electron microscope
200 nanometers
 1 meter = 1000mm

Size:
1mm = 1000 micrometers
1 micrometer=1000 nanometers

 Human - meters
 Human hair - millimeters Naked eye
 Red blood cell - 7 micrometers
 Candida (yeast) - 5 micrometers Light Microscope
 Escherichia coli - 1-3 micrometers
 Herpesvirus - 0.2 micrometers Electron microscope
200 nanometers
Electrons have wavelengths 100,000 times shorter than light.
Can magnify objects over 2,000,000 times (compared with 2000
times for light microscopy).
Electron microscopy - developed 1930/40s
Novel technologies allow visualization of
particles as small as viruses using light
(but not yet in routine use)
Super-resolution microscopy
Expansion microscopy
Virus particle
A Virus
 A set of viral genes
(DNA or RNA)
 Protected by a protein
covering
 May have an additional
covering - an envelope,
derived from the lipid
bilayer membrane of
the host cell.
Enveloped viruses
Non-enveloped viruses
The genome

No of genes
Human >20,000
Bacterium ~ 4000
Herpesvirus ~ 100
Hepatitis B <10

How can so few genes support functions of life?

Viruses have to be obligate intracellular parasites.

The virus replication cycle
 Attachment (adsorption)
 Penetration
 Uncoating
 Viral protein synthesis
 Viral nucleic acid replication
 Virus assembly
 Viral release
Compare with a bacterium:
an independent life form
The Cell

DNA (ds)
Acknowledge EMBL-EBI

transcription (RNA polymerase, nucleotides)

messenger RNA nucleus
messenger RNA cytoplasm
translation (t-RNA, ribosome, amino acids, energy)
Protein
The Cell DNA virus

DNA (ds) Viral DNA (ds)

transcription
messenger RNA Viral mRNA
translation
Protein Viral protein
 DNA Viral replication

The Cell DNA virus

DNA (ds) Viral DNA (ds)

transcription
messenger RNA Viral mRNA
translation
Protein
Image acknowledgement: Han Shan
Viral protein
RNA Viral replication

The Cell RNA virus

DNA (ds)
RNA dependent (-ve RNA)
transcription RNA polymerase

messenger RNA Viral RNA (mRNA)

translation
Protein Viral protein
Retroviral (e.g. HIV)
replication

The Cell Proviral DNA

DNA (ds) Reverse transcriptase Transcriptase

transcription reverse transcription

messenger RNA Viral RNA Viral mRNA

translation
Protein Viral protein
Viruses have learnt to exploit and
manipulate cells
By studying viruses, cell biologists have
learnt a lot (from viruses) about how cells
work !!!!
 Virus Diseases: Definitions
Incubation period: The time interval
between entry of virus into the body and
the commencement of disease symptoms
Incubation period Convalescence

Clinical disease

Infection
 Virus Diseases: Definitions

Incubation period Convalescence

Clinical disease

Viral
shedding

Infection
Period of Infectivity
 Virus Diseases: Definitions

Incubation period Convalescence

Clinical disease

Viral
shedding
Infection
Period of Infectivity
Pathogenesis

A series of events and processes that

combine to produce disease.
Ecology (of virus and host)
Population dynamics (of virus and host)
Transmission
Virus virulence
Types of pathogenesis 1

Localised infections
multiplies at the epithelial surface
at or near the site of entry into
the body
but the disease symptoms may be
local or systemic (e.g. due to
cytokines in influenza)
e.g. respiratory infections
e.g. viral diarrhoea
Types of
pathogenesis 2

Systemic infections:
Initially virus multiplies locally, at
site of entry
then spreads by blood stream
(viraemia) or other means (e.g. along
the peripheral nerves) to distant
sites.
Localises in target organs (tissue
tropism)
Organ damage major disease
Pathogenesis:
Some terms
Viraemia: The presence of virus in the blood.
Acute: in early phase of many disseminated
virus infections
Chronic: eg hepatitis B, HIV
Cell / organ tropism of a virus:
e.g. HIV-CD4 T cell
Mechanisms of viral
disease
Cytolysis (cytopathic effect)
uncontrolled viral replication,
switch off host cell function
induce apoptosis
immunopathological
e.g. hepatitis B: pathology is not direct viral
cytolysis of liver cell. But host immune
response kills virus infected cells.
Induction of tumors (oncogenesis)
e.g. hepatitis B and hepatocellular carcinoma
Viral diagnosis

Detect the virus

Detect the host antibody response

Viral diagnosis:
Detect virus

see - electron microscopy, hours

grow (virus culture in cell lines) - days /
weeks
viral antigen detection - hours
viral nucleic acid detection (e.g.
Polymerase chain reaction) (PCR) - hours
/ days
viral inclusion bodies (histology) - days
Viral diagnosis:
Detect virus

see - electron microscopy, hours

grow (virus culture in cell lines) - days /
weeks
viral antigen detection - hours
viral nucleic acid detection (e.g.
Polymerase chain reaction) (PCR) - hours
/ days
viral inclusion bodies (histology) - days
 Electron microscopy

Need
>106 virus
Particles per mL

Adenovirus in faeces from a

patient with diarrhoea. Also
can detect rotavirus,
Norovirus . . . etc Vesicle fluid from skin or mucosa:
Herpes simplex or varicella zoster
virus
Viral diagnosis:
Detect virus

see - electron microscopy, hours

grow (virus culture in cell lines) - days /
weeks
viral antigen detection - hours
viral nucleic acid detection (e.g.
Polymerase chain reaction) (PCR) - hours
/ days
viral inclusion bodies (histology) - days
Bacteria can be grown in simple
culture media, with no living cells

But viruses will not grow on such

simple acellular media and need
living cells
Grow viruses:
Infect / inject live animals
Virus culture: embryonated egg inoculation
Cell culture

Normal cells Virus cytopathic effect

 Virus transport medium

Virus
transport
medium
CANNOT
be used for
culture of
bacteria

Buffer – pH Protein – maintain virus stability

pH indicator Antibiotics – prevent bacterial overgrowth
Viral diagnosis:
Detect virus

see - electron microscopy, hours

grow (virus culture in cell lines) - days /
weeks
viral antigen detection - hours
viral nucleic acid detection (e.g.
Polymerase chain reaction) (PCR) - hours
/ days
viral inclusion bodies (histology) - days
Viral antigen detection by immunofluorescence
Viral diagnosis:
Detect virus

see - electron microscopy, hours

grow (virus culture in cell lines) - days /
weeks
viral antigen detection - hours
viral nucleic acid detection (e.g.
Polymerase chain reaction) (PCR) - hours
/ days
viral inclusion bodies (histology) - days
Polymerase chain reaction
(PCR)
Amplifies target DNA

Positive result
 Aspects of nucleic acid detection by PCR
Detection of microbial DNA in a If virus is an RNA virus,
clinical specimen by polymerase need to do reverse
chain reaction (PCR) methods transcription step to
convert virus RNA to
complementary virus
DNA (cDNA) before
doing the PCR which
amplifies DNA targets.

PCR amplification and gel detection

PCR amplification and detection of

amplified target using fluorescent signal
emitting compounds  allows
quantification of the microbial gene copy
number – “Real time PCR”
Viral diagnosis:
Detect virus

see - electron microscopy, hours

grow (virus culture in cell lines) - days /
weeks
viral antigen detection - hours
viral nucleic acid detection (e.g.
Polymerase chain reaction) (PCR) - hours
/ days
viral inclusion bodies (histology) - days
Viral inclusion bodies

Negri bodies
In rabies
 Viral diagnosis:
Detect antibody response

Infection Incubation Disease

IgG antibody

IgM antibody
Detect antibody response

A single antibody test? What does it

mean?
Infection at some time during lifetime.
Positive Positive
Infection

Positive
IgG antibody

IgM antibody

Days-weeks Months Years

Detect antibody response
Paired sera 10-14 days apart, tested for
antibody titre (quantitation)
Rising antibody titre: ≥4 fold increase
Titre 1/80 Titre 1/80

Titre 1/20
IgG antibody
Infection

IgM antibody
 Detect antibody response

 IgM antibody
 Recent infection within recent 1-3 months

IgM antibody positive

Infection
IgG antibody

IgM antibody
 • Not all pathogens can be cultured
• No experimental animal models for all diseases
Lecture on Outbreaks
Fredricks & Relman criteria
• A nucleic acid sequence belonging to a putative pathogen should be
present in most cases of an infectious disease and preferentially in
gross anatomic sites known to be diseased, and not in those organs
that lack pathology.
• None or fewer copies of pathogen-associated nucleic acid
sequences should occur in hosts or tissues without disease.
• Sequence copy number of pathogen should decrease with
resolution / recovery of disease and correlates with severity of
disease or pathology
• Organism inferred from sequence should be consistent with the
known biological characteristics of that group of organisms.
• Pathogen sequences should be found in diseased tissue by
methods such as in situ hybridization which can identify which cells
and tissues are infected
• These evidences for microbial causation should be reproducible.
Other types of agents
Defective viruses:

 A virus that does not encode all the structural

proteins required for viral replication.
 Needs a helper virus to provide key genes to
complete virus replication cycle.
Eg.Hepatitis D virus uses the hepatitis B surface antigen
(glycoprotein) as its own surface antigen. But it does not
carry the gene to encode it. Therefore, hepatitis D viruses
can only replicate in hepatitis B infected cells.

See later lecture on Viral Hepatitis

 Prions

An infectious protein

Pro (protein) In (infectious) = Proin=Prion
Not viruses. A completely different form
of an infectious agent.
 Mad Cow disease
 (CJD) Creutzfeldt-Jakob disease

See lecture on Viral CNS infections Brain of patient with CJD

 Reading:

Medical Microbiology: 18th edition, 2012 Edited by

D. Greenwood, M Barer, R Slack, W Irving.
Or new edition Medical Microbiology 19th edition,
2018; Edited by MR Barer, W Irving, A Swann, N
Perera
See:
- Chapter 2: Morphology and nature of
microorganisms (2 pages on The Nature and
Composition of Viruses).
- Chapter 7: Virus-cell interactions.
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