28. Coronavirus 2 Flashcards
why are spikes under immune selection?
immune pressure from Ab causes spikes to mutate
initial monoclonal antibody therapy
used COVID-19 convalescent plasma that has Ab from patient who had recovered from infection
2 examples of therapeutics MAb
- Bamlanivimab
- Bebtelovimab
describe Bamlanivimab
used as early therapy but the virus evolved so became ineffective
describe bebtelovimab
used as early therapy for patients with high risk of disease progression
3 benefits of MAb therapies
- good safety
- moderate efficacy
- good for emergency use when no drugs or vaccines are available
3 downsides of MAb therapies
- resistance mutations in spike
- variants have many mutations that make Ab not effective
- vaccines are better
what was another consideration that had to be made in addition to developing a vaccine that allows the body to make spike proteins?
had to make sure the immune system didn’t react to mRNA
what are the 2 fates of genomic +RNA
- +RNA copied into -RNA for replication
- +RNA copied into subgenomic -RNA
role of subgenomic RNA
to make structural and accessory proteins
mechanism of producing subgenomic -RNA
when viral RNA pol makes -RNA, it can stop at TRS-B btwn each protein and switch back to the leader TRS-L, giving short pieces of -RNA
what does TRS stand for?
transcription regulatory system
4 proteins in RNA replication/transcription complex
- NSP7
- NSP8
- NSP12
- NSP13
what is the most important protein in RNA replication/transcription complex?
NSP12 –> RdRP
role of NSP13?
sits at the top of the complex –> RNA helicase to open up dsRNA for RNA synthesis
what is the role of NSP14? why do we need it?
NSP14 = proofreader
needed bc long genome allows for mutations
what is the co-factor for NSP14?
NSP10
2 activities of NSP14
- 3’ to 5’ EXOribonuclease
- adds methyl group to cap on mRNA
why does the viral RNA have a cap? (2)
- improve viral protein translation
- avoid host immune detection
what are the 2 viral RNA capping enzymes?
both add a methyl:
nsp14 –> guanine-N7 methyltransferase
nsp16 –> 2’ methyltransferase
what happens if NSP16/NSP14 is mutated and there is a bad RNA cap?
body can shut down the virus
what is REMDESIVIR?
Chain terminator –> nt analog that is added to the chain but has no OH so no new nt can be added
targets RdRP
what is MOLNUPIRAVIR?
Increases frequency of viral RNA mutations and impairs replication
how does molnupiravir work?
RdRP uses the drug as a substrate instead of CTP or UTP –> incorrectly incorporates G or A leading to mutation
3 proteins involved in replication factory
- NSP3
- NSP4
- NSP6
where does replication occur and why?
replication occurs in double membrane vesicles to concentrate all components required and shield mRNA from the cell
how do components for replication enter the DMVs?
there are pores/gates for substrates to enter and mRNA to leave
how does the RNA get coated with nucleocapsid protein?
when the viral RNA leaves the DMV via the pores, the nucleocapsid coats the RNA
what is the major component of the replication factory? what is its role?
NSP3 –> protease that cleaves so proteins can mature
3 mechanisms of coronavirus gene expression
- protease cleavage of polyprotein
- ribosomal frameshift
- discontinuous transcription
how does ribosomal frameshift help coronavirus gene expression?
shift by -1 bases to regulate abundance of non-structural proteins
2 components of PAXLOVID
- Nirmatrelvir
- Ritonavir
function of nirmatrelvir
binds nsp5/Mpro –> forming covalent bond so nsp5 cannot recognize protein –> blocks protein processing
function of ritonavir
targets CYP3A4 to increase plasma concentration of nirmatrelvir
where does coronavirus assemble?
in SINGLE membrane vesicle
6 steps of virus assembly + exit starting from replication
- RNA replicates in DMV
- RNA leaves DMV via pores
- structural mRNAs are translated to make proteins
- proteins go to ER and golgi to be glycosylated
- structural proteins meet with mRNA/nucleocapsid at SMV
- particles leave the cell
what protein drives SARS-CoV-2 assembly?
M protein
3 domains of M protein
- N-terminus has extravirion
- 3 transmembrane (TM) domains to anchor in viral envelope
- C-terminus has beta sheet domain (intravirion)
how does M protein form virus vesicle?
M oligomerizes so membrane can curve
- weak interaction with N or RNA individually
- strong interaction with RNA coated by N
this strong interaction can recruit S and E proteins to form virus particle
what is the role of E protein?
Envelope protein: VIROPORIN –> forms ion channel in membrane
- ions move between lumen and cytoplasm
when is E pore open / closed?
low pH = open (golgi)
neutral pH = closed (ER)
what is the general role of N protein?
for RNA binding and packaging
what parts of N protein interact with RNA?
basic parts of N protein interact with RNA
2 parts of N protein, which binds RNA?
N-terminus and C-terminus
C-terminus binds RNA
which 2 non-structural proteins have unknown functions?
nsp2 and nsp11
what is the first protein on the N terminus of the genome? why is it first?
NSP1 –> suppresses host cell translation
how does NSP1 block host cell translation?
NSP1 C-terminus binds mRNA channel in 40S ribosomal subunit so it cannot bind host mRNA
what protease processes NSP1?
NSP1 processed by PL protease
if NSP1 blocks 40S subunit of ribosome, how does viral translation occur?
viral RNA has leader sequence on 5’ end that competes with NSP1 and takes over the 40S subunit to start synthesis of viral proteins
general role of accessory proteins
delay or block immune response in early stages of replication
