Samenvatting
Summary lectures infectious diseases
- Instelling
- Radboud Universiteit Nijmegen (RU)
A summary of all the infectious diseases lectures and some additional information from Mim's.
[Meer zien]Voorbeeld 4 van de 101 pagina's
Voorbeeld 4 van de 101 pagina's
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Voorbeeld van de inhoud
1 Viruses- background, classification, principles1.1 What is a virus
- Huge range of viruses and has the tendency to cause viral outbreaks. E.g. influenza
- Viruses are everywhere; vertebrates, arthropods, plants and fungi all can be infected by it.
o Viruses infect all living organisms.
- What is a virus: ‘a piece of bad news wrapped in a protein’, ‘a package of misinformation’,
‘..trouble in a little protein coat’
Virus discovery: Viruses were first identified by Martinus Beijerinck in the 19th century: filtration
experiments in tobacco industry; virus is smaller than bacterium → ‘contafium vivium fluidum’ =
contagious living fluid (tobacco mosaic virus).
After this other viruses were quickly discovered:
- Yellow fever virus - Influenza
- Rabies virus - HIV
- Variola virus - SARS coronavirus
- Chicken leukaemia virus, poliovirus - MERS coronavirus
- Rous sarcoma virus - SARS coronavirus-2
- Bacteriophage
(Red: first two viruses identified causing cancer)
Definition virus
- Virus; Latin for poison
- Small, obligatory intracellular, infectious agents
- Virus replicates only in host, not in medium
- Fully dependent on a host for on energy metabolism, lipid
biogenesis, protein synthesis
- Virus particles themselves do not ‘grow’ or undergo division,
produced de novo in host
= Obligate intracellular parasites or symbionts that possess their own genomes encoding info
required or virus reproduction and, hence, a degree of autonomy form the host genetic system, but
do not encode a complete translation system or a complete membrane apparatus.
General scheme virus replication cycle
1. Infecting virus attaches to the host cell via a receptor
2. Penetration
3. Uncoating; capsid sheds
4. Replication; synthesis of viral mRNA (direct or via host machinery); synthesis of viral protein
for new capsids; synthesis of viral nucleic acid
5. Assembly; capsids form around nucleic acid
6. Release
a. by budding forming envelope
i. Budding does not necessarily kill the cell but eventually a by-product of
excessive replication may eventually cause apoptosis in the cell.
b. by cytosis, no envelope
7. new infection
1
,1.2 Virus diversity and classification
Viruses are extremely diverse: diversity in genetic make-up replication strategies, virion morphology,
host specificity, disease, etc. = virus taxonomy, to classify viruses. (There can also be diversity within
the sequence variation of virus sequences within a species, e.g. strains or isolates)
ICTV = international committee on taxonomy of viruses
Virus discovery by deep sequencing: Traditionally, virus discovery was initiated upon symptom
development in host organism. In recent years, virome studies using deep-sequencing technologies,
this gave rise to many new viruses, including previously unknown virus families.
1.2.1 Virus classification
Key concept in virus classification: ALL viruses must make +
mRNA that can be read by host ribosomes (no exceptions,
yet)
Although there are 1000s of viruses, there is only a limited
number ways to organize viral classifications → 7
Baltimore classification; based on the type of genome and
its replication strategy
Retroviruses: + ssRNA is transcribed into – ssDNA by viral
reverse transcriptase (carried in the nucleocapsid), dsDNA
is then formed which enters the nucleus and becomes integrated into the host genome. This is then
transcribed by host polymerase into mRNA.
The viral protein is usually ‘monocistronic’, it has one single coding region. It can displace host mRNA
from ribosomes so that viral products are
synthesized preferentially. In the early phase,
the proteins produced are enzymes (regulatory
molecules), that will allow subsequent
replication of viral nucleic acids; in the later
phase, the proteins necessary for capsid
formation are formed.
In viruses where the genome is a single nucleic
acid molecule, translation produces a
polyprotein, which is then cleaved enzymatically
to produce a number of distinct proteins.
In viruses where the genome is distributed over
a number of molecules, several mRNAs are produced, each being translated into separate proteins.
After translation, the proteins may be glycosylated, again using host enzymes.
Viruses must also replicate their nucleic acid: in addition to producing molecules for the formation of
new capsids, the virus must replicate its nucleic acid to provide genetic material for packaging into
these capsid.
➔ Positive ssRNA viruses (e.g. Polio); a polymerase translated from viral mRNA produces
negative sense RNA from the positive sense template, which is then transcribed repeatedly
into more positive strands. Further cycles of transcription then occur, resulting in the
2
, production of very large number of positive strands, which are packaged into new particles
using structural proteins translated earlier from mRNA.
➔ Negative ssRNA viruses (e.g. rabies); transcription by viral polymerase produces positive
sense RNA strands from which new negative sense RNA is produced. In rabies this happens in
the host cell cytoplasm, but in others (e.g. measles, influenzas) replication takes place in the
nucleus – large numbers of negative sense RNA molecules being transcribed for new
particles.
➔ dsRNA viruses (e.g. rota) follows a similar pattern in that positive RNA strands are produced,
then act as templates in subviral particle for the synthesis of new negative sense strands to
restore the double-stranded condition.
One can deduce basics steps in viral life cycle from the nature of the viral genome.
Additional criteria Baltimore
- Nature and sequence of nucleic acid in - Dimensions of virion and capsid
virion - Presence/absence of lipid membrane
- Symmetry of protein shell (capsid) (envelope)
➔ Family classification
RNA viruses (~75%)
- Small genomes (5-3 kb) because viral RNA polymerases lack proofreading activity
- Little space to encode ‘host control’ genes (yet, they often do encode a few)
DNA viruses (~25%)
- Often large genomes (herpesvirus, 120 kb; poxvirus, 375 kb; mimivirus; 1300 kb)
- >50% of their genome dedicated to ‘host control’
Virus taxonomy:
- Realm; Riboviria ➔ Somewhat akin to Linnaean system
- Order (-virales); Picornavirales for taxonomy
- Family (-viridae); Picornaviridae ➔ Virus within family/genus share
- Genus (-virus); Enterovirus overall replication strategy
- Species; Enterovirus C ➔ Viruses within family/genus are not
- Virus: Poliovirus, Rhinovirus, FMDV transmitted the same way, nor do
they cause the same diseases
Take home message
- Viruses are extremely diverse, but can be classified based on genome organisation
(Baltimore)
- Criteria for virus classification
- Virus classification leads to taxa of viruses with shared replication strategies,
- But not necessarily shared host tropism
3
, 2 Detection of viruses and methods for (not only) virus diagnostics
2.1 Detection of viruses
Purposes:
1. Diagnosis for patients with a 3. Epidemiological research
suspected virus infection 4. Surveillance
2. Fundamental scientific research
What does a good diagnostic test have to offer?:
- Delivers a result fast - Is stable
- Is easy to do and interpret - Is sensitive (few false negatives)
- Is financially beneficial - Is specific (few false positives)
Direct vs indirect laboratory diagnostics:
Direct Indirect (serology)
Detection of Detection of
- Whole microorganism (infectious particle) - Antibodies targeting microorganisms in
- Their structural components serum of a patient
o Viral proteins o IgG/IgM
o Genetic material
- Their products
o Mostly relevant for bacteria/fungi
Many of those techniques are also used in scientific research
2.2 Direct methods
- Detect (infectious) virus particles - Detect viral antigen (e.g. envelop
o Culture based techniques protein)
o (electron) microscopy o Antigen ELISA
- Detect genetic material o Fluorescence microscopy
o PCR
o Sequencing
2.2.1 Detect (infectious) virus particles
Virus detection by microscopy
Most viruses are too small to be detected by microscopy, but if you use electron microscopy you
could see some. But it is a difficult technique. You could see virus infected cells. To visualize virus
particles in a sample, electron microscopy needs to be
applied.
Cell culture based detection method
Virus infection can result in structural changes in a
monolayer of susceptible cells, these structural
changes are referred to as = cytopathic effect (CPE),
how does CPE develop:
➔ Some types of CPE are characteristic for a
specific virus infection and allow
identification of the virus: fusion of two cells, ‘owls eye’ (e.g. cytomegalovirus), cells can have
a higher affinity for haematoxylin (e.g. adenovirus), cells die (e.g. Zika die)
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