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H7N9 – Discussion, April 1, 2013 to June 3, 2013 (Closed)

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Re: H7N9 ?Discussion

Re: H7N9 ?Discussion

Out of interest I had a look at the NA & HA alignments for A/Anas crecca/Spain/1460/2008 & the new Chinese sequences and they were surprisingly close on both considering the Partridge was 5 years and half a world away. Both strands - of the new virus - had 5 AA deletion but apart from that the homology was pretty good. So lessons learnt from the paper might apply, at least in similar Chinese birds. Extrapolating to humans would be more of a stretch.
 
Re: H7N9 ?Discussion

Re: H7N9 ?Discussion

could it be asymptomatic with 627E(PB2) ?

no symptoms, very little shedding

only in rare cases E627K evolves and then it's almost always severe

with 627E it would replicate only in some very special cells
 
Re: H7N9 ?Discussion

Re: H7N9 ?Discussion

could it be asymptomatic with 627E(PB2) ?

no symptoms, very little shedding

only in rare cases E627K evolves and then it's almost always severe

with 627E it would replicate only in some very special cells
Are you talking about birds or mammals here?
I am very happy to be corrected here but my understanding was that the change form E to K was a strong mammalian trait and a common adaptation when the virus found itself trying to replicate in a mammal (see post #50 in this thread for a little more detail). I did not know it was associated with severity per se - beyond the fact that once it occurred the virus would reproduce more efficiently in us, which would presumably make things worse for the patient.
 
Re: H7N9 ?Discussion

Re: H7N9 ?Discussion

I mean, in humans.


Fouchier said in a recent interview it increased virulence
1000 fold in ferrets (or mice) afair

searching ...
http://vir.sgmjournals.org/content/88/2/547.full
[equine H7N7] ... with PB2-E627K increasing virulence by 1000-fold as measured by MLD50 [in mice]

How-
ever, from the accumulated data, we conclude that none of the
tested mutations in PB2 had a major impact on the virulence of
A/Netherlands/602/2009 in mice and ferrets. Certainly, for
E627K and D701N, this was in contrast to our expectations,
because a large impact of these mutations was observed in the
context of other influenza viruses in mice and ferrets. In mice
infected with HPAI A/Netherlands/219/2003 (H7N7) virus,
PB2 E627K was the main determinant of pathogenicity, related
to ?1,000-fold differences in lung virus titers (21). Adaptation
of A/Equine/London/1416/73 (H7N7) to mice resulted, among
others, in an E627K substitution in PB2, leading to 1,000-fold-
increased virulence of the virus as measured by the dose lethal
to 50% of infected mice (MLD50) (26). The PB2 E627K mu-
tation was also the main determinant of differences in patho-
genicity of 1997 HPAI H5N1 viruses, in which the MLD50
changed ?1,000-fold upon introduction of the mutation (11).
In HPAI H5N1 viruses isolated from ducks in China, D701N
was the main determinant of pathogenesis in the mouse model
(15). The pathogenicity of a variant of A/seal/Massachusetts/
1/1980 (H7N7) that is highly pathogenic to mice, SC35, was
also determined in part by D701N in PB2 (8). Thus, the mouse
model seems appropriate for testing the effects of both E627K
and D701N in PB2, yet in the context of A/Netherlands/602/
2009 (S-OIV), there was no such marked effect of these mu-
tations on pathogenesis.
There was no major effect
on pathogenesis and transmission of A/Netherlands/602/2009
from any of the three PB2 mutations tested in ferrets

jvi.asm.org/content/84/8/3752.full.pdf
 
Re: H7N9 ?Discussion

Re: H7N9 ?Discussion

so there could be a dramatic effect of E627K in H7 in humans
in theory.
entirely asymtomatic (mild conjunctivitis ?)--> 75%CFR just by one mutation

(?)
 
Re: H7N9 ?Discussion

Re: H7N9 ?Discussion

in that scenario, we might be getting an asymptomatic pandemic now with
some mild cases and some severe cases and quite some deaths.
Did that ever happen in human history ? A worldwide wave of
pneumonia deaths without a detectabla flu-wave.
Horse H7N7 was very old, not avian.
We need the H7-serology from Shanghai !
 
Re: H7N9 ?Discussion

Re: H7N9 ?Discussion

Gs I do not know enough about why it caused the great increase noted to make a helpful comment, beyond the fact that, as noted earlier, having the correct version of 627 can radically changes the expression of viral protein. In this case it already has the version best suited to protien expression in humans so a change at that position back to E would be a good thing - for us. What I would take from the extract is how dependent the effect is on the genetic background. And in the same vein I would expect at least as large a variability if you changed the host from mice to human. H1N1(2009) functioned quite happily in humans despite having the 'wrong' version.

The section below is a very basic explanation of the the function of this strand which I hope will help anyone who is following this thread but does not have a biology background. I would recommend reading post #50 first as it follows on from that. In it I said that flu is a negative sense single strand RNA virus (-ssRNA) but never explained what that means or why it is significant. Human genetic material is stored in double stranded DNA where the two strands are handed one being positive and the other negative. The positive strand is 'read' to make an RNA equivalent in a process called transcription. This RNA strand is then translated into a sequence of amino acids which form the coded protein. This Youtube link is to a short (4 mins) graphic visualising the process. Flu's problem is its RNA is wrong handed, being negative, and so it needs a bit of machinery the host can not supply. The RNP discussed in post 50 is this missing link and allows the production of a positive RNA which can be used by the host to make viral proteins.
This is obviously a gross simplification but I hope it will show that RNP is not an H7N9 RNP in that its function is largely independent of the surface proteins whose numbers (7 & 9) denote the serotype - although it must work in concert with its other proteins and some RNPs may be a better fit than others. In the case of the H7N9 of concern in China the RNP related RNA strands recently came from an H9N2 virus which is still circulating in birds.
 
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Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

I have been having a look at the latest Chinese human H7N9 sequence release A/Zhejiang/DTID-ZJU01/2013 and there are a few points of interest.
Firstly it is very similar to the other released sequences generally where the Shanghai/1 sequence varied from the others this one is more like S2 and H1. The two strands of interest where it does vary are PB2 and NA.

Starting with PB2 it has K627 which puts it a odds with all the other mammal sequences (they have E627) but in-line with the birds. I don't find this odd as I have been arguing that the most likely scenario is that birds are the host reservoir with K627 and that the human infections from birds start with that but select for E627K mutations as they work better in mammals. The second change is more interesting it is D701N. This is also a mammalian trait and improves the viruses' RNP's ability to traverse a mammalian cell's nuclear membrane which it needs to do to get to where it becomes biologically active.
I do not know if the NA changes have any biological significance they are all close together (possibly a recombination event?) and as far as I know well away from the Oseltamivir binding pocket but I would like someone more knowledgeable to confirm that (a lack of numeric proximity need not imply the amino acids are not adjacent in the tertiary protein structure).
The NA changes are W434L, S437G & N438D.
One other change I noted was on NS T170I.
All the numbers are as per the alignments and may differ from other numberings.
Edit:
Does anyone know of a good numbering off sets table for all strands?
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

R292K in NA? S31N in M2? Polybasic cleavage site in HA1-HA2? NS1 c-terminus...?
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

R292K in NA? S31N in M2? Polybasic cleavage site in HA1-HA2? NS1 c-terminus...?
I did not see any changes apart from those I listed and I had a look at most strands, including NA, M2, NS1 and HA. Nothing odd on PB1-F2 either.

Edit :
Sorry Giuseppe it does have S31N but so did all the others so it is not a change.
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

Curiously has anyone considered bats as the carrier of the H7N9 virus?
I thought of this as I hosed down the side of my house which often gets splattered with bat feces which is very runny and mucusy.
Shanghai has a large bat population as does the entire region; studies have shown that their genes can be immune to deadly bugs and act as a reservoir for viruses like Ebola and SARS.
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

it looks more and more to me that the main H7N9+H9N2 reassortment
happened early this year, that S1 is just strange, with mutations
acquired during prolonged disease or sequencing errors.
The same for Z2 in HA and maybe some others in NA.
We had such things before.

The remaining meanwhile 8 genomes with 3 excluded
subsequently reassorted segments and one partial HA
show a smooth picture of constantly evolving flu-A
since the initial reassortment ,probably in Jan.2013,
as we know it from other outbreaks.

that dating coincides with the Chinese new year poultry-movements
by humans and may even indicate the outbreak is human made,
nondeliberate, of course. Someone may have had a wild duck in his poultry cages.

Of course, it could also just have been wild birds droppings or such.
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

Two more sequences, HA only, one chicken & one goose both from Jiangsu.
The goose has R65M (R56M using H3 numbering) but other than that no changes.

Out of interest I thought I would query the GSAID database to see what the dominant avian serotypes in China were. I limited my search to 1/1/2010 or later.
Chickens returned several hundred sequences with H9N2 very dominant.
Ducks about 100. H9N2 also dominant but a lot more other subtypes so significantly more variation.
Geese 7 with 3 H5N1 and the others all different.
Turkeys, Quail, Guineafow and Paserines all none.
The 'other birds' category had 3 returns the current H7N9 pigeon, and two H9N2s an egret and our Bramling which has featured in this thread.
I ran the alignments for the egret and the bramling on the RNP genes and they are very different with 60 amino acid changes across the 4 strands.
Given the dearth of available sequence it is amazing we found the Bramling which is such a good match for the internal gene sequences.
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

Given the dearth of available sequence it is amazing we found the Bramling which is such a good match for the internal gene sequences.
Since Bramlings can be pets in China, it's good that they're testing them. I'd ask whether they are "caught" out of the wild population or raised in captivity - that information would be important.

.
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

http://tomkellie.zenfolio.com/p140980056
which migrate relatively long visitors, and are a late autumn and winter visitor to Beijing
(sampled Nov.07.2012)

> Here I show a report of winter birds in Beijing botanical garden by Beijing bird watching society.
> They indagated four times and recorded 39 species .
> 35 Brambling
> Some part of river thaws. it becomes a good place for bird drinking(of course ,for watching)
> I just stay here 15min and see some good birds.
> 100 Brambling (I try to find one Chaffinch from them, but i fail)
Feb.29.2008




either way - it likely caught it from poultry
 
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