Diagnostics 2- Virology Lab Flashcards
Name 4 things that can be tested for in the virology lab
- Infectious virus
- Protein components of the virus(antigens)
- Genetic components of the virus
- Host response (antibody / cell responses)
Cell culture and electron microscopy are rarely done these days. They have been replaced by
PCR
Name 3 diagnostic methods used nowadays
- Antibody detection (serology - Enzyme Immunoassay (EIA))
- Antigen detection (Immunofluorescence - IF, or EIA)
- Genome detection (using PCR)
What are the limitations of lab tests
Give false negative and false positive results
What is sensitivity and specificity
Sensitivity = tests ability to correctly identify positive samples
Specificity = tests ability to correctly identify negative samples
Name 3 things that can be quantified during diagnostic Virology tests
- Antibody
- Antigen
- Genomes
What is viral load
Amount of virus present in blood/other fluids
Name 5 viruses that quantifying the genome is essential for diagnosing and monitoring in the immunocompromised
- HIV
- HCV
- HBV
- CMV
- EBV (glandular fever)
Genome sequencing may help direct treatment towards specific viruses. What 2 things may be involved with genome sequencing
- Genotyping
2. Antiviral resistance testing
Name 7 types of samples used and what they’re used for
- Throat swab/Nasopharyngeal Aspirate (NPA) / Bronchoalveolar lavage (BAL)/ ET secretions - used to detect respiratory viruses by PCR
- Stools - for rotavirus, adenovirus or notovirus, by PCR
- Urine - for BK virus by PCR
- CSF - for herpes viruses and enteroviruses by PCR
- Clotted blood - obtain serum for serology (antibody detection)
- Blood (EDTA to get plasma) - for PCR/Viral load testing
- Saliva - for PCR/serology
What is serology used for
To test for specific antibody viral antigen
Give 3 examples of serology tests used
- HIV serology - test for antibody and p24 antigen
- HBV surface Ag/b, eAg/b, core Ab, core IgM
- VZV IgG
Which antibody is the marker for acute/recent infection
IgM (approx 3 months)
Which antibody indicates past infection or immunisation
IgG
IgM has a low specificity. What does this mean
High rate of false positives
HIV serology testing is one of the main ways to test for HIV. It involves a 4th generation EIA that tests for which 2 things
- Ab
- p24 antigen
(Reactive species undergo confirmatory testing in 2nd assay to exclude false positives. Then confirmed positives undergo typing (HIV 1 vs HIV 2). Then repeat blood sample and EDTA blood for HIV viral load)
What is the benefit of point-of-care testing
Immediate results for HIV or RSV - works with lab testing doesn’t replace it
(Less sensitive than lab testing)
Virus isolation in cell culture is rarely used as a diagnostic means because it is time consuming and expensive. However, what is it still useful for?
Phenotypi antiviral susceptibility testing (HSV)
Electron microscopy is also rarely used. What sample types does it work for?
Stool and vesicle fluids
What is immunofluorescence used for?
Direct detection of viral antigens in clinical samples (e.g. respiratory viruses)
It is rapid and cheap but subjective - depends on quality of sample and technicians skill
Name 3 respiratory tract infections
influenza, RSV, rhinovirus
What does multiplex PCR allow
Testing multiple viruses in each tube
What samples and tests are done is there is a suspected CNS disease (meningitis/encephalitis)
- CSF for PCR (HSV, VZV, Enterovirus)
- Stools and throat swab for enterovirus detection (by PCR)
- Blood for serology and/or PCR for West Nile / Japanese Encephalitis Virus and other arboviruses
What things must be established in the clinical history for suspected CNS disease
- Meningitis (inflammation but no changes to brain i.e. no confusion) or encephalitis (inflammation with accompanying changes)
- Young child with febrile fits
- Immunocompromised
- Recent travel to endemic region
- In context of an outbreak
- SSPE (measles antibody index)
What samples for diagnosis are taken if there is diarrhoea and vomiting
- Stool (preferred)
- Vomit (has lower yield)
PCR or antigen detection assays (EIA) done
What do enteric viruses do?
Cause diarrhoea/vpmiting
e.g. norovirus, rotavirus, adenovirus, sapovirus, astrovirus
What is PCR for and what is the starting block used?
Used for amplifying target RNA or DNA sequences
dsDNA is the starting block
At what temperature is the RNA cycled (taq polymerase can withstand)
95 degrees
It is cycled through steps with various temperatures
What are the sequencing applications of PCR?
- Genotyping
- Antiviral resistance testing
- Phylogenetic analysis
What are the different types of PCR
- RT-PCR
- Real time PCR
- Multiplex PCR
- Viral load testing
- Sequencing (antiviral drug resistance testing)
