Virology Lab Flashcards
What is a maculopapular rash?
Some areas are raised and some areas are flat
What is a dermatomal distribution of a rash indicative of?
Shingles
What components of the virus can be used in virus detection?
Virus isolation and electron microscopy to visualise the virus itself
Protein components (antigens)
Genetic components (RNA or DNA)
The host response (antibody or cell responses)
What is the main method of virus detection?
PCR
What technique is used for antibody detection?
Enzyme immunoassay – detects antibodies and antigens
Define sensitivity
Test’s ability to correctly identify positive samples
Low rate of false negative
Define specificity
Test’s ability to correctly identify negative samples
Low rate of false positives
What does quantification of the genomes allow assessment of
Viral load (amount of viral nucleic acid present in bloods/fluids)
Diagnosis and monitoring of HIV, HBV and HCV + CMV and EBV in immunocompromised
Compare IgM and IgG
Both present in acute phase of disease
IgM- 3 months (recent infection)
IgG - lifelong (rises later)
IgM often gives false positives - avidity testing used to test strength of antibody binding
What does positive IgG and absent IgM indicate
Past infection or immunisation
Describe the process of HIV testing
4th generation EIA
Antibodies and p24 antigen
All reactive samples undergo confirmatory testing in a second assay to exclude non-specific reactivity (false positives)
What other investigations are performed on people who are identified as HIV positive
Typing (HIV 1 or HIV2)
Repeat blood sample and EDTA blood for HIV viral load (for genotyping and baseline resistance testing)
What test is used to confirm a positive IgM result
Antibody avidity testing
Describe how antibody avidity changes in infection.
Early on in the infection, avidity is LOW
Then you get maturation of the antibody response so the avidity will increase over a period of 3-6 months
If you have HIGH antibody avidity, then it is unlikely that the infection occurred in the last 3 months
What is immunofluorescence useful for
Direct detection of viral antigens e.g. resp
Rapid and inexpensive but subjective and very dependent on the skill of the technician and the quality of the sample
What is the term given to the method of PCR that allows testing for more than one virus using a single test tube
Multiplex PCR
What samples are used for detection of respiratory viruses
Throat swab
Nasopharyngeal aspirate (NPA)
bronchoalveolar lavage (BAL)
ET secretions
What can stool and urine samples be used for
Stool - rotavirus, adenovirus, norovirus antigen detection (EIA) or PCR
Urine - BK virus and adenovirus PCR
What can CSF and blood (clotted and EDTA) samples be used for
CSF - for herpes viruses and enteroviruses PCR
Blood (clotted) - for serology (antibody detection)
Blood (EDTA) - for PCR / viral load testing
What can saliva samples be used for
Serology and PCR e.g. measles
Give examples of types of virology testing
Cell culture
Electron microscopy (EM) -
Antibody detection e.g. anti-HIV antibody (Enzyme Immuno Assays)
Antigen detection (IF, EIA) - HBsAg in hepatitis B infection or RSV antigen in respiratory sample
Genome detection –PCR to detect viral DNA or RNA
Quantification of antigens and genomes (now essential for diagnosis and monitoring of HIV, HBV and HCV)
Genome sequencing: Genotyping, Antiviral resistance testing
Give the advantages and disadvantages of virus isolation in cell culture
Useful for phenotypic antiviral susceptibility testing (HSV)
Slow and time consuming and therefor expensive
Describe electron microscopy
Viruses are small but can be visualised using an electron microscope.
Sample types of stool and vesicle fluids
Rarely used
What tests should be ordered for a suspected respiratory tract infection
Throat swab +/- nose swab Nasopharyngeal swab Nasopharyngeal aspirate (NPA) Bronchoalveolar lavage (BAL) Endotracheal tube (ET) secretions - all for respiratory virus multiplex PCR*
What tests should be ordered for a CNS disease, for example meningitis and encephalitis
CSF for PCR (HSV, VZV, enterovirus)
Stools + throat swab for enterovirus detection (i.e. by PCR)
Blood for serology and/or PCR for West Nile and/or Japanese Encephalitis virus infection and other arboviruses
What tests should be ordered for diarrhoea and vomiting
Stool (preferred) or vomit (but lower yield)
PCR or antigen detection assays (EIA)
Enteric viruses causing diarrhoea/vomiting = norovirus, rotavirus, adenovirus, sapovirus, astrovirus
Describe the method for PCR
- dsDNA or Viral RNA converted to dsDNA using reverse transcriptase from retroviruses
- Denature at 95 degrees
- Primer annealing
- Chain elongation by taq polymerase
- Cycle x30
What are the uses for the products of OCR
Genotyping
Antiviral resistance testing
Phylogenetic analysis - investigate outbreaks/transmission
What are the types of PCR
RT-PCR Real Time PCR (different to above) Multiplex PCR Viral load testing Sequencing (antiviral drug resistance testing)
