Flu Flashcards
How many genes are there in flu?
17 - many are in other ORFs through splicing variants, ribosomal frame shifts or alternative initiation sites (8 segment in the genome)
What are the advantages of flu replicating in the nucleus?
Can do cap snatching as there are many around. May not be as many RNA sensors, but starting to think there my be some RIG-I in the nucleus
How does flu enter cells?
HA binds sialic acid. Entry through endosomes and pH sensor reveals the fusion peptide through a conformational change in HA2. For this to occur, need cleavage of HA by a protease (amino acid sequence in HA depends on the specificity of the protease and whether the virus can be cleaved anywhere or just by proteases found in upper airways). The M2 ion channel unlocks the capsid.
What is the structure of the RNP?
A nucleoprotein every 20 nucleotides
Describe the structure of the flu RdRp
3 subunits - PB2, PA and PB1. PB2 binds the cap, PA is the endonuclease (cleaves the cap) and PB1 does polymerisation. The heterotrimer has a different structure (at the 627 domain orientation) depending on whether it is bound to RNA or not.
How does flu switch from transcription to replication?
Thought to be due to small viral RNAs. Know need NEP (NS2). Could be due to RdRp that is newly synthesised having a different structure and therefore being seen differently by host factors
What determines the specificity of avian flu to birds (and not humans)
The PB2 subunit of the polymerase. Need a mutation - E627K for avian viruses to replicate efficiently in human cells
Why can’t the avian flu polymerase work efficiently in human cells?
Could be a negative factor in human cells or a positive factor in avian cells. Found that fusion of avian and human cells activated the polymerase - a positive factor. Screened avian chromosomal fragments in hamster cells to find the gene - ANP32A. Avian ANP32A has an extra 33 amino acids compared to humans
What is the significance of ANP32A?
In birds has an extra 33 amino acids, and it is this that prevents the avian polymerase functioning in human cells. Has functions in transcription control and histone modifications. In infection, we know it binds the polymerase, including the apoenzyme (with no RNA bound). It may load the RdRp onto the genome, but this isn’t known.
How does the flu particle leave the nucleus?
NP needs to be unphosphorylated by a host phosphatase, then self assembles around RNA genome. Matrix then binds and other proteins aids funnelling of genome out of the nucleus.
How does the flu particle assemble?
After segments have left the nucleus, specific packaging signals in the terminal regions some how talk to each other and come together to ensure there are 8 vRNPs in the virion - loops of genome push between NP and talk to each other and line up. This then pushes through the plasma membrane which already contains flu proteins HA, NA and M2. M2 cytoplasmic till mediates membrane scission.
What is the function of NA?
Cleaves sialic acid as virus leaves cell so it doesn’t stick. Is a tetramer with an active site.
What are the drugs against NA?
Neuraminidase inhibitors are Relenza (zanamivir, inhaled) and Tamiflu (oseltamivir, orally taken). Were intelligently designed to take advantage of features of the active site e.g. charges. All current strains are susceptible (though resistance can and has been seen to develop - a pandemic displaced the resistant virus)
What is the controversy against Tamiflu?
Has been stockpiled by governments incase of an outbreak. Has been suggested that the drug isn’t as effective as thought and that there were flaws in the trial and side effects. However, the trials were done in a normal flu season, whilst it was shown retrospectively that during the swine flu pandemic treating with tamiflu quickly could half the risk of death - potentially a problem with doctors being willing to administer the drug.
What mutations are required for avian flu to become pandemic in humans?
Receptor specificity - in upper airways we have alpha 2-6 linked sialic acid (only have alpha 2-3 in lower airways, so can infect and get serious pneumonia but isn’t transmissible )
HA has to be stable for airborne transmission - pH needs to be lower as we have a mildly acidic respiratory tract (virus needs to be inside cell before uncoating). Also makes virus slower to leave the endosome in the cell which could lower case fatality percentage. Also, distance of spread is increased in human population compared to a poultry farm where rapid uncoating is good for rapid spread.
Virus has to pass mucous barrier in humans - needs a longer NA stalk to be able to cleave soluble sialic acid in mucous
