Lc8 - virology

Question 1

HIV - general

Answer 1

• Retrovirus –> ssRNA –> reverse transcriptase –> DNA
• HIV-1 clades:
  o M (major) has subtypes (CRFs)
   C – 50%
   CRFs – 18%
   A – 12%
   B – 10% (western world)
  o O (outlier)
  o N (new)
  o P
• HIV-2
  o A-H
  o Only A and B are epidemic (west Africa and portugal)

Question 2

HIV replication

Answer 2

Early phase:
1. VAP: gp41 and gp120
Target: CD4 and CCR5
o Later stage the coreceptor is CXCR4
2. penetration
3. uncoating
4. reverse transcription (error prone)
5. nuclear import of preintegration complex DNA
6. DNA integration

Late phase
1. transcription viral genes
2. translation
3. gal polyprotein etc.
4. assembly
5. budding
6. maturation

Question 3

new HIV staging

Answer 3

based on:
- absolute CD4 count per uL
- CD4%
- presentation of AIDS defining diseases

AIDS: <200 c/uL / <14% / yes

Question 4

acute HIV infection

Answer 4

1. Infection via sex or needles etc.
2. Attaches to DC
3. DC goes to lymph node
4. Infects macrophages, active CD4 and inactive CD4 cells
5. Once the CD4 cells is active it starts to produce virions
6. Virions are released and infect other cells  normally initially in the GALT
   - During this period PreP can work

Question 5

Biomarker profile HIV infection (feibig stages)

Answer 5

1.viral RNA
2. p24 protein
3. anti-HIV env protein antibodies
4. anti-p31 antibodies

Question 5

CD4 loss - HIV

Answer 5

• Gut CD4 cells are lost within months which leads to mucosal infections and high bacterial load
  o This high bacterial load leads to inflammation (systemic) which causes a high turnover rate of CD4 cells in the blood leading to their slower decline than GALT CD4 cells
• After 6 months a steady state is reached – this includes a set viral load
  o Low viral load leads to low CD4 loss and slower progression
  o High load –> fast progression

Question 6

quasispecies

Answer 6

• Since replication of retroviruses is very fast and sloppy approx. one mutation per replicative cycle occurs
• This leads to large differences between virions of an individual host (quasispecies) –> contributes to immune evasion
• During sexual transmission only the fittest particles can leave the genital tract meaning that upon infection an individual receives a very ‘strong’ quasispecies from the previous individual –> sexual transmission bottleneck
• Quasispecies development is faster than production of antibodies –> immune evasion
  o Some individuals will after 3 years finally have developed broadly neutralising antibodies

Question 7

chronic HIV - dynamics

Answer 7

• CD4 cells in HIV patients have a high turnover rate  every 2 days they replicate which contributes to 93-99% of viral production
• Memory cells –> 1-7%

Question 8

CD4 cytotoxicity

Answer 8

o Direct cytotoxic effect
o Indirect (only 1:1000 cells are infected but more die)
 Hyperimmune activation (due to GALT destruction)

And reduced production by thymus

Question 9

lymphoid damage

Answer 9

• Due to HIV sustained inflammation causes fibrosis of LNs
• This impairs the interaction between APCs and lymphocytes
• Also the structure of the reticular network is worsened over time

Question 10

cART

Answer 10

• Aims to reduce the viral load and prevent loss of CD4 cells by inhibiting viral replication
• Blood plasma virus concentration <50 RNA copies per mL
• cART: 3 drugs combined
  o 2 NRTI + INSTI/PI/NNRTI +pharmacokinetic enhancer (CYP inhibitor)

Question 11

clinical features - COVID

Answer 11

• Lung: pneumonia and cytokine storm
• Heart: myocarditis
• NS: encephalopathy, anosmia, dysgeusia
• GI: nausea, vomiting, diarrhoea
• Kidney: renal failure
• Blood vessels: thrombi, emboli

Question 12

general virology - COVID

Answer 12

• Enveloped
• VAP: spike glycoprotein
• Hemagluttinin-acetylestrase glycoprotein
• Membrane glycoprotein
• Small envelope glycoprotein
• (+)ssRNA
• nucleocapsid phosphoprotein

Question 13

variants - COVID

Answer 13

• Changes in the receptor binding domain of the spike protein leads to higher or lower transmission and immune evasion
• Delta was crazy transmissible –> all parts of the world had slightly different variants at different timepoints until delta hit
  o Higher binding affinity
  o Higher viral production

Question 14

replication - COVID

Answer 14

1. spike-ACE2
2. cleavage TMPRSS2
3. uncoating
4. translation of RNA replication proteins (nsps)
5. RNA replication
6. translation of structural proteins
7. assembly in ER vesicles
8. release by fusion

Question 15

mRNA - vax

Answer 15

lipid nanoparticles with spike protein mRNA
fast short lived humoral response (4-6 it drops of fast)
cellular response is longer lived >8months

Question 16

adjuvanted protein - vax

Answer 16

spike protein subunit (produced by yeast of bacteria) with an adjuvant
injected and presented by muscle cell

Question 17

vax platforms

Answer 17

1. mRNA
2. inactivated virus
3. adjuvanted protein
4. adenovirus vector

Question 18

adenovirus vector

Answer 18

non-pathogenic virus is used to deliver covid spike gene
longer lastig humoral immunity but slower initial response