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

[Pathfinder]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

Reposted from:
http://www.flutrackers.com/forum/showthread.php?t=204095

H7N9 virus can be traced to 3 bird species: Chinese expert

2013/04/17 20:30:20

Beijing, April 17 (CNA) The deadly H7N9 avian flu virus can be traced to three bird species -- a brambling from Beijing, fowl in the Yangtze River Delta and a wild bird from the Korean peninsula, according to a Chinese scientist.

Xue Yu, a professor at Huazhong University of Science and Technology in Wuhan in central China, said his research team reached the conclusion about the three bird species after completing an analysis of the H7N9 virus's genetic makeup.
...
Sometime before last November, he said, the H9N2 carried by a brambling from Beijing interacted with the H7N3 virus carried by fowl in the Yangtze River Delta.

"Each of these two species provided three genes to form part of the H7N9 virus. These six genes alone, however, would not sicken humans," Xue said.
Roughly at the same time, a duck in Zhejiang Province in the Yangtze River Delta provided hemagglutinin (HA) to turn the above-mentioned genes into H7N2/N3, Xue said.

"This was a critical step for the virus to get the key to infect or invade human or animal cells," Xue said.

In the third stage that took place around Feb. 19 this year, a wild bird from the Korean peninsula brought in the most important element, neuraminidase (NA), to complete the H7N9 virus's genetic makeup of eight genes, Xue said.

"NA allows the virus to spread freely in its host," Xue said.
...
"When we get more samples, we will be able to better understand the evolution of the H7N9 virus," Xue said, adding that the conclusions may be adjusted or even changed fundamentally.
...
http://focustaiwan.tw/news/aedu/201304170035.aspx

 

[NS1]

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.

Jiangsu Wet Market Surveillance Analysis - Available.

Analysed the emergent H7N9 gsChinaJiangsuK27_2013_04_01 HA 65M as 51M and discussed positional polymorphic behaviour to Lysine in related sequences from GenBank and GISAID.

• Sequence Analysis - Open-Access, Full-Text
• GISAID Citation

 

[AlaskaDenise]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

Brambling information with range map here.

The reported habitat sounds like my backyard.

added: Bramblings were spotted in Seward, AK on January 27th! It was really cold. They're year round residents, as reported here. The referenced blog reports the first sandhill cranes arriving and headed over the hills to the north - they should be here soon, but we still have 3 to 4 feet of snow on the ground (melting fast).

.

 

[Pathfinder]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

Brambling



This bird is widespread throughout the forests of northern Europe and Asia. It is migratory, wintering in southern Europe, north Africa, north India, northern Pakistan, China and Japan.[1] It regularly strays into Alaska during migration and may continue as far south as the western United States...

This species is almost entirely migratory. In Europe, it forms large flocks in the winter, sometimes with thousands or even millions of birds in a single flock. Such large gatherings occur especially if beech mast is abundant. Bramblings do not require beech mast in the winter, but winter flocks of Bramblings will move until they find it. This may be an adaptation to avoid competition with the Chaffinch.[4] Bramblings mostly eat seeds, but unlike most finches, their young are fed largely on insects. It builds its nest in a tree fork, and decorates the exterior with moss or lichen to make it less conspicuous. It lays 4-9 eggs.
http://en.wikipedia.org/wiki/Brambling
------------------------------------------------------------------------

http://birds.audubon.org/birds/brambling

 

[AlaskaDenise]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

Some of the migration and range data is outdated because climate change is influencing their habits. Birders here are noting the arrival dates are about 2 weeks earlier and more birds are being found in new locations.

.

 

[JJackson]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

There have been a few more sequence releases so I thought an update might be in order. On the E627K change we are continuing to get E in the birds, and environmental samples, and K in the humans (apart from the one instance already covered) so I continue to think there is strong selection pressure - on this background - for this change once a human is infected.

Of the new human releases there are two but they only cover HA, NA & PB2. I have placed them all in the table below which is going to need a bit of explanation.
The A1, S1, S2 etc. in bold across the top are abbreviations for the sequences Anhui(A), Shanghai(S), Hangzhou(H) & Zhejiang(Z) with the numbers being taken from their full sequence names.
Down the left we have the proteins in bold (HA, NA & PB2) and below each is the positions at which a change has occurred with the consensus amino acid at that position. In the body of the table is the change.
So the first row of the HA block shows R65 as the normal value and the only Sequence with a change at that point is Shanghai1 which has M65 (R65M). The colours and other highlights I will cover below.

All the sequence numbers are as they align but you will see in various threads discussion of Q226L as being a significant change but this is in the H3 numbering system and for these (H7) sequences you need to add 9 (NB This +9 only applies to the HA sequences) so 226 becomes 235 which has L on all bar S1 (having Q) and H1 (I).

Now for the colours.
Red is for sites of know biological significance (mammalian adaptation).
Green is for changes that have occurred more than once.
Blue is for the weird multiple changes on Shanghai1's HA which looks like they may be lab generated error as they are not coming up anywhere else and are too dispersed over the length of the strand to be easily accounted for as a recombination event.
The sequences with a box around them are adjacent, or very nearly adjacent, on their strand and could be recombinations which had occurred in that host rather than from the infecting strain. I am assuming they can be safely ignored.

I will ignore the Blue and Boxes as being insignificant (until proved otherwise) and discuss some of the Red and Green areas.

Lets start with the Reds.

HA 235 (or 226 if you prefer)
Almost all the avian and environmental samples (which I have not included in the table) have Q and almost all of the table samples have L which is Leucine. The two exception are Shanghai1 (which is still the bird type Q) and Hangzou1 which is I. This is interesting because I is Iso-Leucine which is chemically very similar to Leucine (and along way form Glutamine (Q)) which adds weight to the argument that the virus is trying to adapt within its host and this one has found something better than Q but not quite hit on L yet.

PB2 627
Unlike HA235 this is not occurring within the new host. Although it is a 'mammalian marker' it is also in the avian sequences so the birds are coexisting happily enough with it so, on this genetic background, it would seem not to be severely selected against in birds and is also fine in humans.

PB2 701
This was discussed in post #72 but again looks like it is the virus adapting to its new host.

Now for the Greens.
I do not know any of these positions as being of great import but as more sequences become available it will be interesting if these continue to occur as they may imply that there are strong selection pressures to achieve these changes - or it may be a fluke - time will tell.

 

[AlaskaDenise]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

On today's Dr. OZ show, Dr Besser (CDC) talked briefly about H7N9. He was part of the experts that recently went to China.

Dr. OZ asked if he thought the reports about H7N9 were hyped and Dr. Besser answered NO! He briefly said this was a very serious influenza that needed to be taken seriously, although not now in countries outside China. He put considerable emphasis on his opinion that professionals and countries need to get ahead of this problem and prevent its spread. He stated that prevention is the key, not treatment.

THis program is very popular in the US, so we can assume his words will reach a large audience.

I couldn't find a video to post.

.

 

[gsgs]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

jjackson, don't we arrange the viruses vertically, one virus per line
and the mutations horizontally, one position per column, no ?

S1 was unusual

 

[Giuseppe]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

A new NEJM paper discusses epidemiology and results are quite different from things we heard so far. http://www.nejm.org/doi/pdf/10.1056/NEJMoa1304617

 

[Vibrant62]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

A new study on H5N1 suggests that the Q226L mutation makes the H5N1 virus lose its fitness in birds (and therefore may explain why this virus has not further adapted to humans over the last decade), yet this does not seem to be the case for H7N9. This mutation has been seen in avian sequences.

This tends to illustrate the point that just because mutations have a specific effect in one virus, it does not necessarily confer the same characteristics in another.

But Gamblin speculates that the virus’s abandonment of its avian past may allow it to evade components of human mucus called mucins, which are structurally similar to avian receptors. Normally, mucins glom onto flu viruses and tie up the grappling hooks, preventing hemagglutinin proteins from latching on to cells. Because the Q226L mutation destroys hemagglutinin’s ability to recognize bird receptors, it may allow the virus to slip past the mucins and get right to cells, aiding in transmission, Gamblin says.

This mutation also carries a potential upside for people: Because the mutant H5 can no longer bind to avian cells, viruses carrying the mutation probably would not be able to replicate in birds, Gamblin says. That could mean that the mutant virus may not be able to jump directly from birds into people. Instead, to pick up the mutation and become transmissible by air, H5N1 would first have to infect — and reproduce in — people or another animal. So far, only the laboratory created strains of H5N1 can spread through the air, and they contain other mutations that adapt the virus to live in mammals.

http://www.sciencenews.org/view/generic/id/349926/description/Mutation_makes_H5N1_flu_lose_its_grip

 

[gsgs]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

what's different

 

[JJackson]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

gsgs

jjackson, don't we arrange the viruses vertically, one virus per line
and the mutations horizontally, one position per column, no ?

I did not realise I was breaking with convention and just chose to display it that way. Is it a 'always put the time on the x axis' sort of thing?

Vibrant62

This tends to illustrate the point that just because mutations have a specific effect in one virus, it does not necessarily confer the same characteristics in another.

I tend to meet this again and again which is why you keep finding my postings peppered with 'on this genetic background' caveats. I have noticed a general tendency to say SNP x has effect y but always mentally add a 'usually'.

As to

what's different

That is tricky. Vibrant's quote may explain one reason for that particular case but my guess is that more generally it relates to induced changes in the proteins tertiary structure which I discussed in more detail as part of this old post. I have pasted a chunk below but the full post can be found at the link (as it was a reply to questions relating to antigenic sites it is stressing that aspect but the point of posting it here is to show the folding mechanism and how it controls form and so function).

By a process of transcription and translation the codons of genetic information in the HA gene are converted into the amino acid sequence of the HA protein. This is a string of amino acids, like links of sausages, (protein's primary structure) but it immediately forms bonds between the side chains on the amino acids so the 'sausages' form sheets or spirals or other structures, this is the protein's secondary structure. The secondary structure then forms further bonds to each other with hydrophobic bits hiding in the middle and hydrophilic bits on the outside. This final Tertiary structure is not coded for in the genetic sequence and is, infact, dependent on the environment in which it forms. It is also not fixed if you change the pH, or other properties of the medium the protein is in, it will reconfigure (or more likely just flex a bit). This can be a very important biological property, for instance the weak binding of oxygen to heamoglobin for oxygen transport uses this. IF a change at one base caused a change in an amino acid at a point which then caused a different build of the secondary, and subsequent Tertiary structure, then it COULD cause all the antigenic sites to be presented differently. It is hard to envisage a scenario in which this could occur and not have such profound affects on the proteins biological function that it rendered it non-viable but as no one knows what would or would not be viable it is THEORETICALLY possible. The point of change in this scenario need not even fall within any of the antigenic sites, it need only cause a change effecting more than one of them. If you look at the nucleotide sequences for the antigenic sites (table in previous post) you will see that they are not a contiguous block due to the folding described in the section on secondary structure.
The graphic below is taken from the paper linked to at 1] as it shows the secondary structure (twirly ribbon bits) and then for the primary antigenic sites it attempts to show the 'solid' surface (grape like clusters). The whole concept of 'solid surface' is a manifestation of our macro scale world and does not really apply on this scale. Biological molecules are more fuzzy and 'feel' each others electrical surfaces being attracted, repelled and forming bonds of different types and strengths.

The above is of NA, for a change, but there is also one for HA if you follow the link.

 

[gsgs]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

well, usually you'd have long virus names and in Western cultures we read
left to right, not top to bottom.
And 3 nucleotides make one amino-acid, easier to spot horizontally.
I'm used to those vertical "lines" in the mutation tables, indicating clusters of common mutations

 

[gsgs]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

the secondary,tertiary structure only depends on the amino-acids,
on the HA-proteins that have a direct task.
But then we have the encoding of those in nucleotide sequences
and I think one of my first questions here was, whether it matters
how we encode the amino acids in nucleotide-RNA-strings.
Apparently not so much .. (?!)
The bird-index is very different in America and Eurasia
at the nucleotide level, but identical with amino acids.
We can just "set" the probabilities for amino-acid mutations
by appropriate encodings

 

[Missouriwatcher]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

According to Nature Worldwide, (birds of Missouri) the brambling stay in the area during the winter, while its primary nesting range is elsewhere.
http://www.birdlist.org/checklists_o...f_missouri.htm

You-tube has a video of the brambling seen in Morrison, CO (near Denver) on Nov, 20, 2012.
http://www.youtube.com/watch?v=CMZDkfKU7WI

 

[JJackson]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

the secondary,tertiary structure only depends on the amino-acids,
on the HA-proteins that have a direct task.
But then we have the encoding of those in nucleotide sequences
and I think one of my first questions here was, whether it matters
how we encode the amino acids in nucleotide-RNA-strings.
Apparently not so much .. (?!)
The bird-index is very different in America and Eurasia
at the nucleotide level, but identical with amino acids.
We can just "set" the probabilities for amino-acid mutations
by appropriate encodings

Once you have an amino acid sequence, coded from a nucleic acid sequence, there is no difference and it is impossible to tell what bases were on the RNA strand just by looking at the Protein (or AA sequence). If the American and Eurasian sequences are different at the nucleotide level, but identical at AA, then it is because the protein 'works' and is selected for regardless of the sequence that created it. The sequence of bases is helpful in determining 'parentage' relationships but is immaterial biologically - assuming no AA change.

 

[gsgs]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

well, for the proteins, yes.
E.g. there are 500? HA-proteins ("spikes").

But then we have the 8 segments, encoded, encapsulated into
ribonuclein complexes, and these also have some 2ndary, 3ary
structure, and then these must be opened and copied and
transported,transcripted,translated,packed


there are multiple copies of each of the 14 proteins included in one virus
PB2:30-60
PB1:30-60
PA:30-60
HA:500
NP:1000
NA:100
M2:20-60
NS2:130-200
PB1-F2:2650
M1:3000
NS1:NA
PA-X
???????
from
Cox,Neumann,Donis,Kawaoka: Orthomyxoviruses:influenza
http://www.topleyandwilson.com...
table 32.2 , page 10

http://www.annualreviews.org/doi/abs/10.1146/annurev.bi.52.070183.002343?journalCode=biochem
http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.52.070183.002343
http://hedrick.ucsd.edu/BIMM114/Reference-Neumann--influenza.pdf
page 14

 

[JJackson]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

PB1-F2:2650

I had not seen that number before. That is an awful lot of PB1-F2 considering that the second reading frame is not even open in all flus so it is biologically optional, at least on some backgrounds.

 

[NS1]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

Once you have an amino acid sequence, coded from a nucleic acid sequence, there is no difference and it is impossible to tell what bases were on the RNA strand just by looking at the Protein (or AA sequence). If the American and Eurasian sequences are different at the nucleotide level, but identical at AA, then it is because the protein 'works' and is selected for regardless of the sequence that created it. The sequence of bases is helpful in determining 'parentage' relationships but is immaterial biologically - assuming no AA change.

The illogical, but much promoted, myth that differences are not different always concerned our team.

Five years ago, we began discovering high correlation codon variance to host species when the amino acid value was held constant. H3N8 provides numerous HA sequences that demonstrate strong correlation for host species class (mammalia v aves) to different codons coding for the same amino acid. Those correlations are not all attributable to Influenza ancestry.

 

[JJackson]

Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

I am sorry NS1 but I did not understand what you were saying in your post. That certain species tend to use one triplet while another species uses an alternative. e.g. Glycine can be coded for GGx where x is any of the four alternatives and in birds x is usually different to mammals? If that is what you are saying then I have no problem with that and it is not at odds with what I wrote. If you are saying that the finished protein is in anyway different please post back because that would mean I have badly misunderstood something (by no means impossible) and I need to work out what lest I mislead anyone else.