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

[gsgs]

Re: H7N9 ?Discussion

someone with access to the GISAID-sequences should really publish his/her reassortment-chart
It's needed (IMO) to access the risk of the strain evolving in mammals.
Publishing reassortment charts should not violate the GISAID rules.
It's a responsibility to mankind that GISAID members have, IMO :
to share the pandemic relevant info with the public (mostly nonmembers).
It could be urgent, remember how Peiris said we may have a small time-window to wipe it out.
We can't wait for the papers to be published which takes years.
It's not very likely IMO (~~5%?) that this will evolve into a pandemic, but likely enough that
we should consider it seriously.

[gsgs]

Re: H7N9 ?Discussion

if this were indeed all happening in some nonpoultry species, then that might explain
why we see no sick poultry. If that species were mammals or rodents or quail or such,
that might also explain the increased prevalence of these mammalean markers.
But, due to the differences in mutation counts in the segments that would also
imply subsequent reassortments with other strains that so far we only know
from chicken-H9N2 (and a brambling).
That would mean either a frequent exchange of segments between this species
and poultry H9N2, ongoing since years or a big diversity of many years of evolution
in that species already.
Or that species could be wild birds or semi-wild ducks.
That would not explain the mammalean markers but would explain how H7N9 came in
and make the diversity and prolonged H9N2 evolution more plausible and explain
why we see no sick birds.

[JJackson]

Re: H7N9 ?Discussion

I have been looking at more of the analysis being produced at http://epidemic.bio.ed.ac.uk/influenza_H7N9 and they are all useful. I would recommend Tommy Lam's analysis which has all 8 trees with the AA changes annotated at the branch points. This makes it easy to see what sequence changes occurred causing the divergence.

Samantha Lycett's analysis puts both the NA & HA last common ancestor estimates at mid to late 2011 and uses the NA stalk deletions to suggest the N9 component has spent some time in poultry.

[gsgs]

Re: H7N9 ?Discussion

yes, if we assume there was just that one reassortment with HA,NA, which seems reasonable,
then it looks like a creation of the strain ~1 year ago.
But then we have bigger similarities in PA,MP,NS indicating a common anchester only
1/2 year ago. So these would have to be transferred by another reassortment.

It's not soo significant, though. Few mutations. Could be random.
But the differences in NP are bigger, that one should really have been
acquired by subsequent reassortment.

[JJackson]

Re: H7N9 ?Discussion

While the contributors to this thread are mainly FT regulars most of the readers are non-members and some of the more technical posts may be confusing. With the caveat that I am no expert and know what I know - or think I know - from reading at FT and linked papers. The following will, I hope, help clarify some of what is being discussed. If you know any of the following to be wrong please post corrections.

Flu is a negative sense encapsulated single stranded RNA virus with 8 RNA segments which, usually, code for 11 proteins. If we look at these 8 strands they are
M - which codes for the Mo protein which is cleaved into two biologically active parts M1s which link to form the capsule, giving it its spherical or elongated shape, and M2 which is embedded in the M1 shell and acts as an ion pump. The pump changes the pH after the virus has entered the host cell causing the M1 shell to rupture and release it contents. The action of M2 is the target of the Amantadine anti-viral drugs.

H - codes for the HA protein which sticks through the viral wall with a head 'outside' and the tail 'inside' the virus. The exposed external part has the main antigenic sites which may, or may not, be recognised by your immune system depending on prior exposure. Functionally it is responsible for first binding to the host cell and then penetrating the cell wall.

N- codes for NA which, like HA, projects through the viral wall. It also has antigenic sites although they are less important than those on HA. Functionally it is key to the release of new virus particles as they exit the cell. This process is the target of the Neuraminidase inhibitors like Oseltamivir (Tamiflu).

M, NA and HA between them give us the shape and surface structures visible in an electron micrograph.

NS1 - the non-structural protein seems to be involved in a number of intra cellular process notably on the intra cellular immune response by suppressing Interferon production.

Which leaves us with the Polymerase complex proteins encoded in PB1, PB2 & PA and the Nucleoprotein NP.
PB1, PB2 and PA combine to form a single functional protein which then combines with the NP to form a Ribonucleoprotein (RNP) which transcribes (reads) the negative RNA strands so the host cell can be conned into producing new virions.

The graphic below (taken from) shows different views of the polymerase complex in the top two rows and the whole RNP at the bottom where you should be able to identify the complex on the left of the left image (compare to view A) and on the right-hand end of the right image (as seen in image C).


A number of the post in this thread talk about H7N9 showing signs of mammalian adaptation and one of these changes is on PB2.
A change from Glutamic acid (E) to Lysine (K) in the 627th amino acid (E627K) causes a change in the optimal operating temperature of the RNP. The avian (E) form likes it a few degrees warmer than the mammalian (K) form and when the E (bird) form grows in a mammal then the NP bonds more weakly to the P-complex and there is measurably less viral protein expressed.
Please note that what applies on one viral background may not apply on another, or at least not to the same degree.

Looking at the cladograms linked to in my last post the Bramling differs from the H7N9(2013) by just the E627K change on PB2 (discussed above).
On PB1 again one change I525V.
On PA two changes K356R & D394N.

The situation on the NP strand is a lot more complicated indicating a more complex mutation path, and probably a further reassortment. It splits the H7N9 sequences and leaves the Bramling perched on a remote branch. Shanghai1 (S1) has M239V, D375E, V406I & V408I non of which are found on S2 or A1 and they both have I371M, which S1 does not.

Hoping it helped and did not just add to the confusion. JJ

[JimO]

Re: H7N9 ?Discussion

^^^Excellent summary! Thank you.

[gsgs]

Re: H7N9 ?Discussion

you still need a reservoir in poultry as a base where this thing
reassorts with other (poultry-)strains and evolved since
creation, probably ~1 year ago.

E627K and Q226L - like mutations have been reported in the past
to occur sporadically, inside the very host.
So we don't know if these transmits.
And if, then it must be silently since we have no long known transmission chains.

I mean, a new strain evolving in some other host like pigeons or swine
would have to be quite new (probably some months) while H7N9 would
have evolved and reassorted silently in poultry for ~1 year since creation.
But if it had evolved for 1 year, then it probably still is there and they
should find it in poultry.

or a strain evolving parallel in birds/poultry and mammals, jumping back
and forth ... but we never saw that in the past

[AlaskaDenise]

Re: H7N9 ?Discussion

NPAI or HPAI can be silent in pigeons, then have fatal mutations as shown in tests mentioned in this post: http://vet.sagepub.com/content/43/4/463.short

.

[AlaskaDenise]

Re: H7N9 ?Discussion

Racing pigeons are usually vaccinated for Newcastle and many of the Newcastle vaccines also include influenza. Vaccinating a sick bird can sometimes precipitate the very disease in the vaccine. Given that some countries do combination AI vaccines, there may have been some vaccine issues with racing pigeons, who then race accross international borders. China produces plenty of AI vaccines. Pakistan enjoys pigeon racing and produces combination AI vaccines. There is one from Italy: BIO FLU? H7N1+H5N9.

.

[gsgs]

Re: H7N9 ?Discussion

we have this well known H9N2 reservoirs and evolution in poultry.
The current H7N9 is on this background.
With HA and NA gained from another pool, that we don't know much about.
International wild bird HA and NA mixing organisation.

But the other segments can be traced. And it's hard to imagine for me
genetically, that there is another reservoir where evolution happens secretly.

At least they would have to continually exchange sequences back and forth.

Unless it were a very recent "separation".

[Oric]

Re: H7N9 ?Discussion

In a overcrowded planet of humans, i would not be surprised to see mammal evolution to start with humans bypassing rodents and swine

[sharon sanders]

Re: H7N9 ?Discussion

Welcome back Oric!

[AlaskaDenise]

Re: H7N9 ?Discussion

Oric....our "boots on the ground hero"??? Good to "see" you.

.

[JJackson]

Re: H7N9 ?Discussion

Yes nice to see you posting again Oric. Your help at the time of the H5N1 Turkish clusters was invaluable.

[gsgs]

Re: H7N9 ?Discussion

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045332/

LPAIV subtype H7N9 (A/Anas crecca/Spain/1460/2008).
neither clinical signs nor histopathological findings were observed in
A/Anas crecca/Spain/1460/2008?H7N9 LPAIV infected partridges