discussion

[gsgs]

goes here, or start a new thread

[sharon sanders]

Re: antigenic avian influenza evolution is mainly restricted

Is the common distant ancestor an amoeba?

[Sally Furniss]

Re: the birdflu index virus

How did you calculate it? Is it an average of some chosen sequences? What sequences did you use? What selection criteria did you use in choosing the sequences

[Sally Furniss]

Re: antigenic avian influenza evolution is mainly restricted

why would antigenic avian influenza evolution be mainly restricted

in several inner segments of influenza A we typically only see limited (~10)
amino-acid changes in wild avian flu so that these segments are close to the calculated
"index"-protein-sequence here:
http://www.flutrackers.com/forum/sho...d.php?t=135205
Synonymous changes are not affected and do occur at normal rates.

No such restriction is observed in mammalean flu,
which accumulates ~2.5*10^-3 nucleotide changes
and ~4*10^-4 amino-acid changes per position per year.
(6 nucleotide changes and 0.8 amino-acid changes in PB2 per year in humans)

and mammalian flu not restricted

[gsgs]

Re: discussion

> Is the common distant ancestor an amoeba?
no, an influenza virus

> why would antigenic avian influenza evolution be mainly restricted
> and mammalian flu not restricted
yes,why. Anatomy,host genetics,or way of transmission

check the ducks. Ducks can be wild or poultry, unfortunately in the
database it isn't usually marked whether the ducks were poultry or wild.
Sometimes we have "wild duck" , but I assume most ducks are poultry
and wild ducks are usually "mallards".
Keep mallards or pintails as poultry in one farm and monitor their flu.

[gsgs]

Re: the birdflu index virus

How did you calculate it? Is it an average of some chosen sequences? What sequences did you use? What selection criteria did you use in choosing the sequences

the bird index is just the average of all avian sequences
in that segment.
At each position the amino-acid used in most of the sequences.
There could be cases where this has to be modified because of
bias towards one strain, but I felt that so far this wasn't necessary.

H5N1 has relatively many mutations away from the index in most
segments and there are lots of H5N1-sequences at genbank,
so this is a candidate for such bias.

For HA and NA I felt that H3N8 is the most likely index=origin,
next likely candidate would be H4N6, so I took H3 and N8.
For NS I took NS1 but I have another index for NS2

[gsgs]

H5N1 in poultry vs. wild birds

looking at the index-distances ...

the 1997 Hongkong outbreak was caused by a poultry virus in most segments.
The virus had proably evolved since decades in poultry as LP in H6N1 or H9N2.
Hard to say where HA and NA came from - poultry or wild birds.
There is few index-like behaviour in HA.

The 1959 H5N1 outbreak in Scotland was from a much wilder virus.

Then H5N1 reassorted in 2002,2004 with wild viruses and all our modern
H5N1 in Vietnam,Japan,Indonesia,Qinghai is caused by wilder viruses,
still not as wild as 1959.
As ancestor of modern H5N1 I would consider A/Ck/Henan/16/2004. The HP H5-HA
is still from the early poultry outbreak, but inner segments are wilder.

Prevent the mixing of poultry viruses with wild bird viruses.
I.e. in China ducks and geese.
Same for swine.
Keep poultry and swine away from wild birds with flu.
We would still have the old adapted viruses, but no reassortment and refreshment
from outside.

Make regular reassortment tests of poultry viruses with the index-virus.

Test whether amino-identical index-viruses with entirely different
nucleotide-sequence show different reassortment behaviour.

[gsgs]

Re: discussion

http://www.ncbi.nlm.nih.gov/pubmed/20399567

when HA and NA did split into the 16 resp. 9 types:

> 1411-1932 of the Common Era (AD) for haemagglutinin
> and 1366-1874 AD for neuraminidase.


what was before that ?
bottleneck in mallard-evolution because of little icetime ?