Clinical virology Flashcards
Types of infection
i) acute infection
ii) latent infection
iii) progressive infection
iv) chronic infection
Where is the next emerging virus going to come from?
animals
What is the one health concept?
Look into animal health and see how it interacts with human health
How can animals spread zoonotic virus to ppl?
i) direct contact
ii) vector (mosquito)
iii) indirect contact
iv) food
How to detect the level of desired DNA formed?
use probes
—> higher cycle threshold value is equivalent to less DNA —> less virus
What does high Ct value infer?
less nucleic acid —> fewer viruses
Molecular testing used for viral infection
q-PCR of RT-PCR (For RNA viruses)
Advantage of using PCR
i) able to test multiple viruses at once (multiplex)
ii) little hands on time
iii) gd turnover time
iv) available in many labs
v) lots of samples can be done at once
What does turnover time mean?
time needed to get the results
Drawbacks of using PCR for viral infection
i) costly
ii) cannot test for immunity (only test the virus)
iii) highly dependent on specimen quality
iv) need to go to reference centre for confirmation
Example of probes used in detect of DNA in PCR
- non specific (Sybr Green)
- specific ones (Taqman)
Steps to design PCR for viral infection
i) design primers to target specific region of virus
- target one or more viruses?
ii) include primers and probes (control)
iii)determine the sensitivity and specificity levels
iv) check with clinical samples
Why primers and probes are needed in PCR?
as a control to make sure the sample is not degraded
Why we need to check for specificity of PCR test designed?
make sure it specifically tst for this virus
—> not detecting other closely related virus
What can u do if u cannot get the samples u want for PCR?
test to see if other methods of getting samples can also be used for testing
Why is important to know viral genome?
used in diff. categories
- develop molecular diagnostics
- template for vaccine
- help with epidemiology studies
- understand viral evolution and transmission
Two types of whole genome sequencing
i) metagenomics
ii) amplicon based
Factors to consider when using sequencing
i) coverage (how much of the genome should be sequenced)
ii) depth (the level of detail in sequencing)
What happens if you prioritize depth for genome sequencing?
discover rare variants….
Major steps in whole genome sequencing
i) library prep (prepare DNA samples needed + tags to identify them)
ii) sample amplification
iii) get sequence through identifying signals
iv) bioinformatic analysis (see if it belongs to any known family)
How can bioinformatic analysis help in whole genome sequencing?
- characterize the virus
- reduce epidemiologic uncertainty
metagenomic vs amplicon based sequencing
i) amplicon one order the genome in order after sequencing
ii) metagenomic just sequences the whole thing without order
Why metagenomic sequencing is preferred over amplicon sometimes?
i) no info known to the virus
—> cannot do amplicon based sequencing
Prep before doing whole genome sequencing
i) generate cDNA or genomic DNA into smaller parts
ii) include barcodes (tags for multiplexing)
What are barcodes in wgs?
unique DNA tags to certain virus
how is barcodes used in whole genome sequencing?
tag DNA which allows sequencing of multiple types of DNA in same cycle
How does whole genome sequencing determines sequence?
i) records fluorophore signal at each position
ii) use this to identify and order the bases
—> each base have different color
How is WGS used in Covid?
i) identify different strains
ii) determine if patients are infected by same or different strains of Covid
What is serological testing?
detect specific antibody against infecting organism
What can serological testing used to identify viral infection?
see if it’s acute, recurrent or past infection depending on their ability to bind
advantage of serological testing
i) cheap and easy
ii) can go through lots of samples at once
drawbacks of serlogical testing
also indicate previous exposure, not just active infection
which antibody indicates acute infection
IgM
Which antibody indicates resolving infection
igG