Virology [Complete]

Question 1

What features can we detect in suspected viral infection?

Answer 1

Infectious virus (by isolation or electron microscopy)

Protein components (antigens such as p24 antigen in HIV)

Genetic components (RNA or DNA)

Host response (antibody or cellular response)

Question 2

What are the main methods of diagnosing

Answer 2

Cell culture and electron microscopy (replaced by PCR)

PCR (Polymerase chain reaction): [Detectes genome]

Detects specific sequences of DNA.

Antibody detection:

Serology (EIA = Enzyme Immunoassay).

Antigen detection:

Serology (EIA and IF = Immunofluorescence).

Quantification of antibody or antigen.

Serotyping – i.e. in HIV.

Quantification of genomes – viral load.

Genome sequencing – genotyping and antiviral resistance testing.

Question 3

what viruses is genome quantification used for?

Answer 3

HIV

HBV

HCV

CMV/EBV

In the immunocompromised.

Question 4

What are the limitations of lab tests?

Answer 4

False negatives due to sensitivity

False positives due to specificity

Question 5

What is sensitivity

Answer 5

Ability to correctly identify positive samples

Question 6

What is specificity

Answer 6

Ability to correctly identify negative samples

Question 7

What types of samples can be taken and when would they be taken?

Answer 7

For detection of respiratory viruses by IF or PCR:

Throat swab

Nasopharyngeal aspirate (NPA)

Bronchoalveolar lavage (BAL)

ET (Endotracheal tube) secretions for PCR.

Stools: For detection of rotavirus, adenovirus, norovirus for antigen detection (EIA) or PCR.

Urine: BK virus and adenovirus for PCR.

CSF: herpes viruses and enteroviruses for PCR.

Blood: (clotted) for serology (antibody detection)

Blood (EDTA) :for PCR / viral load testing.

Saliva for serology and/or PCR (e.g. measles).

Question 8

What is the difference between IgM and IgG in terms of when theirlevels rise following infection?

Answer 8

IgM is a marker of RECENT infection

IgG rises later on in the infection and some remains after the infection has passed

Question 9

What is IgM a marker of?

Answer 9

Recent infection

Question 10

What is IgG a marker of?

Answer 10

As it is created later in host response it lasts longer and indicates an infection which occured earlier

Question 11

When are IgM and IgG made and when do they usually peak?

Answer 11

Both created in acute phase of disease.

IgM peaks early and drops off after a few weeks while IgG only get higher and plateau

Question 12

What is looked out for in HIV

Answer 12

Antibodies

p24 antigen

Question 13

What is looked out for in Hep B?

Answer 13

IgM and IgG

Question 14

What is looked out for in HBV

Answer 14

Surface Ag/Ab

eAg/eAb

Core Ab

Core IGM

Question 15

What is looked for in HCV

Answer 15

Antibody with or without core antigen

Question 16

What is looked for in CMV,EBV, MMR and parvovirus B19

Answer 16

IgM and IgG

Question 17

What is looked for in VZV?

Answer 17

IgM

Question 18

process of HIV serology testing

Answer 18

4th gen: Currently detects antibody and p24 antigen

Positive result goes into confirmatory test to reduce false positives in an assay

Confirmed positives undergo typing for HIV 1 or 2 - samples repeated and EDTA blood for viral load (for genotyping and resistance testing)

Question 19

What does positive IgG and absent IgM indicate?

Answer 19

Past infection or immunisation

Question 20

what can confirm a positive IgM result?

Answer 20

Antibody avidity test

Question 21

What is avidity?

Answer 21

Strength at which antibodies bind to a specific antigen

Question 22

Describe how antibody avidity changes in infection.

Answer 22

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

Question 23

What is viral isolation used for despite being time consuming and expensive

Answer 23

Phenotypic antiretroviral susceptibility test

Question 24

what is immunofluorescence used for? What are the advantages and disadvantages?

Answer 24

Direct detection of viral antigens typing and cell culture

Advantage: rapid and inexpensive

Disadvantage: produces subjective results dependent on the skill of the technician

Question 25

What is the term given to the method of PCR that allows testing for more than one virus using a single test tube?

Answer 25

Multiplex PCR

Question 26

What samples are collected in resp tract infection? How are these samples then used?

Answer 26

Throat swab

Nasopharyngeal aspirate (NPA)

Bronchoalveolar lavage (BAL)

ET (Endotracheal tube)

Then do multiplex PCR with multiple viruses in one tube

Question 27

What 4 things are sampled when testing for meningitis/encephalitis?

Answer 27

CSF

Stools​ and Throat swab (for enterovirus detection)

Blood

Question 28

What is additionally tested for in CNS diseases depending on the following conditions:

Menningitis and encephalitis

Febrile fit (Young child)

Immunocompromised

Recent exotic travel

Outbreaks

Answer 28

Meningitis or encephalitis: HSV, VZV and enterovirus.

Young child with febrile fits : Add HHV-6 + parechovirus.

Immunocompromised (HIV): Add CMV, EBV, JC virus.

Recent exotic travel: Japanese encephalitis, West Nile virus, equine encephalitides, tick borne encephalitis

Outbreaks: depends on context e.g mumps

SSPE: Measles antibody index

Question 29

what sample is taken for diarrhoea and vomiting?

Answer 29

Stool (preferred)

Vomit (low yield)

Question 30

what can be detected in vomit by PCR or EIA

Answer 30

Norovirus

Rotavirus

Adenovirus

Sapovirus

Astrovirus

Question 31

What must happen first before PCR is performed to identify the genome of an RNA virus?

Answer 31

The RNA must be reverse transcribed by reverse transcriptase to dsDNA

dsDNA is the start point of PCR

Question 32

Describe the process of PCR to amplify RNA (RT-PCR for RNA) or DNA

Answer 32

Carry out 30 cycles usually

Starting block is dsDNA ( if the initial virus has RNA, use RT-PCR to form dsDNA).

Denaturing the dsDNA into strands by heating.

Taq polymerase elongates the chain.

Cycles induce exponential expansion.

“Real-time” PCR produces a read-out of results.

Question 33

How can outbreaks be investigated?

Answer 33

phylogenetic analysis

Question 34

What needs to be done to select the correct antiretroviral drugs

Answer 34

Antiretroviral resistance testing with genotyping

Question 35

What are the applications of sequencing viral genomes?

Answer 35

Antiviral resistance testing

Phylogenetic analysis