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Summary Advanced Medical Microbiology - Test 2 (Virus part)

Name: Advanced Medical Microbiology - Test 2 (Virus part)
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Author: nadinevankleef

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Universiteit Van Amsterdam (UvA)

This is a small summary for the course Advanced Medical Microbiology from the master Biomedical Sciences at the UvA. It includes all the information you need for the first test of this course including lectures from van Marit van Gils, Neeltje Kootstra, Tonja van der Kuyl, Colin Russel and Hans Zaa...

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4 items

1. Samenvatting - Advanced medical microbiology - test 1 (virus part)
2. Samenvatting - Advanced medical microbiology - test 2 (virus part)
3. Samenvatting - Advanced medical microbiology - test 3 (bacterial part)
4. Samenvatting - Advanced medical microbiology - test 4 (bacterial/parasite part)
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Usutu virus
In the Netherlands we only have two arboviruses, tick born encephalitis virus and Usutu virus
(record holders)

Usutu virus originated from Afrika (1959), it was a cycle between birds and Culex pipiens (mosquito,
gewone huissteekmug). It is in Europe since 2001, common blackbirds (merel) started dying. It was
also found in some bats. A few clinical cases are described, especially when it is an
immunosuppressed/haematological patient.

Many arboviruses are completely asymptomatic. Some have medium to severe disease and people
can die from yellow fever virus. Not all arboviruses are flaviviruses, however, Usutu virus is.

Usutu is irrelevant for humans because its most often asymptomatic, it can however cause neuro-
invasive disease in some cases. Why does Sanquin check it for blood transfusions?  West Nile
virus.

There are 4 areas of West Nile endemics in Germany (Berlin area). As soon as you have 1 patient
with West Nile Fever  stop collecting blood or check everyone. It is very dangerous  probably
die (majority of blood recipients are immune compromised). Next summer  probably comes here
in the Netherlands (screen for this).

Usutu virus cross reacts in all PCRs with West Nile virus, it is not that specific and they really look like
each other.

 Flaviviruses are horribly cross reactive in ELISAs. There is also cross neutralisation, antibodies
inhibit culture of other flaviviruses.
 If you start West Nile screening, big chance its only Usutu virus. You have to look into it 
and make sure patient is treated.
 Last year there were more West Nile cases than all the years before that, or was it Usutu?
You don’t get ill from Usutu  based on really old papers (you thought it was a hangover but
it was Usutu?).

Cycle West Nile Virus: Bird  mosquito  human/horse. Human & Horse are dead end hosts
(cannot give it to anyone else). Last year the West Nile Virus crossed the Alpes, horses were positive
 sometimes humans follow. However, not-spreading was stable for 40 years.

Many blackbirds died in the Netherlands  regions free of blackbirds. Blackbirds are not the most
suitable host for the virus since the virus wants to spread. Dying blackbirds are a good indicator for
presence of virus, but not necessarily the main host.

We know exactly how many blackbirds died when/where  crazy bird watchers. In 2016/17/18 a
lot of blackbirds died. No rain in heatwave last year  no birds dying because mosquitos want little
bits of water to lay their eggs.

Monitored 3 provinces with a high blackbird density. They kept spare samples of blood donors,
tested for Usutu/West Nile Virus. There was a little bit of cross reaction in differentiating PCR
between Usutu and WNV when using specific primers. Usutu virus was in the donors, 1 in 700
random people infected.

 Estimate incidence rate: Length of viremia (2 months, 1/6 chance per year). It is only present
in parts of the year, divide by 4. Only 1 person in the population.

,  PCR tested 7 NL donors that were positive, they carried 2 lineages of Usutu, europe3 and
afrika3.

Serology: Coated ELISA plate with envelope of Usutu, worked pretty well to detect IgG and IgM. For
some Usutu virus infected humans, you see that the test for antibodies against West Nile Virus
worked better.

What happens when you transfuse blood of Usutu virus positive donors? 3 patients received red
blood cells (2) and platelets (1), not plasma since virus is inactive there. The recipients were immune
competent. They did not show seroconversion  did not infect recipients.

Tested serology on 1000 donations  11 positive for Usutu virus antibodies. Donors with medium
IgG, high IgM were positive for Usutu Virus in the past. However, can also turn out to be a reaction
against another flavivirus.

 Sensitivity is good, specificity is not good.

This year hardly any dying of birds  only 2 weeks ago birds started to die  do not study it yet.

Summary:
 August 2018 in NL: ~ 1:700 donors in central Holland were USUV viremic.
 Endemic USUV will interfere with WNV testing and donor-screening in the Netherlands.
 No sign of USUV-infection in 3 exposed recipients. To be studied with greater power?
 Impact of USUV as a pathogen? Proposed: retrospective study of the role of USUV in Dutch
patients with unexplained neuro-invasive disease.
 Next year in a mosquito near you: WNV.

Hepatitis C virus
It is an enveloped +ssRNA virus. It infects the liver causing hepatitis. Has been around for centuries.
They found it after a transfusion, was not hepatitis A or B.

Hepatitis C belongs to the flaviviruses, but it is not mosquito borne. They are classified in the
hepacivirus, they only infect humans and chimpanzees.

 There are also Pegivirus (hepatitis G) and Pestivirus (non human viruses)

HCV genome organisation: RNA, 10kb (not very big or small). Encodes for one single polyprotein. It
is digested by protease where it encodes for.

HCV replication cycle:

1. Entry: Lipoviral particle with lipoproteins binds to several
receptors & enters via endocytosis. During endocytosis
membranes will fuse.
2. Uncoating: Particle will be uncoated.
3. Translation & polyprotein processing: RNA goes into
cytoplasm of the cell  to ribosomes  translated into
polyprotein  cleaved  proteins make sure there is
formation of membranous web.
4. RNA replication: Virus is starting to replicate. +ssRNA will be translated into -ssRNA
(intermediate) and then into +ssRNA.
5. Assembly: Positive strand with core proteins will be encapsidated

, 6. Release: Bud out of the membrane of the cell.

It uses an RNA dependent RNA polymerase. Lack any proofreading  many mistakes  high
mutation rate  defective virus or virus with selective advantage. You get new genotypes &
subtypes. There are different clusters. In the genotypes are subtypes. Very high variability.

Prevalence: All over the world, high prevalence in Africa & Asia. Region specific distribution of
genotypes.

 Egypt: Very high prevalence (15-20%) caused by vaccination programme where they used
unsterile needles, vaccinate against liver disease caused by schistosomiasis. Hepatitis C was
now the cause of liver disease.

Transmission: Blood-blood contact.

 Risk group Netherlands: Injecting drug users, recipients of blood bank products before
testing (1992), tattooing/piercing, needle stick injuries, men who have sex with men,
migrants from endemic countries.
 Endemic countries: Circumcision, traditional scarring, traditional tattooing, acupuncture.

Pathogenesis: During acute infection its mild to
asymptomatic (looks like flu). 20-25% of infection
is resolved, 75-80% develop chronic infection 
risk for liver cirrhosis, hepatocellular carcinoma
(HCC). Disease progression can be fast (<20 years)
or slow (> 30 years).

Treatment: We want to get rid of it because during the
whole period you are not sick, you are able to transmit it.
Goal: Sustained virological response  not detect it
anymore in blood. There are non responders,
breakthrough (resistance to treatment) and relapse.

Options:

IFN-alpha/pegIFN: Give it to patients, antiviral effect & boost immune system. You get sick from the
interferon & long time. 16% cleared the infection.

Ribavirin: Guanosine analogue blocking viral RNA synthesis. Worked better, especially in
combination. 40%-55% cleared infection. Very though treatment, long time.

Direct acting antivirals (DAA): Targeting viral enzymes (protease, polymerase). The more you
include  the better it gets. 2 months, 97% clear infection.

 You can get re-infected, you are not protected by previous immune response.
 1 pill DAA costs more than 1000 dollars  LOT of money. In third world countries its too
expensive, here we can pay it.

DAA has disadvantages: Most of them have high efficacy. There is also genotype specificity, most of
them are only good against genotype 1. Genetic barrier: How easy/difficult is it for virus to adapt to
presence of medication. Protease inhibitors have a low genetic barrier  chances of mutation that

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