Tuesday, May 14, 2013

man-made pandemics


for better formatting and possible later editing and additions and graphics
and responses and discussion ]
profvrr wrote on 2013.May.13 in response to DavidS
> Animal models are not predictors of what will happen in humans.

somehow they are.That's why we are using them, why you say "it's good science"
You probably meant: are not so good predictors (as most think)
> We study infections in animals to obtain mechanistic clues;
you say mechanistic clues, I'd say probability estimates
> conclusions about what happens in people require further testing. There are dozens
> of examples of this in the literature. Drugs and vaccines are tested in several animal models,
> but are the drugs and vaccines then released for humans? Of course not; clinical
> trials are done.
which often however confirm the animal tests. I'd guess in ~70% of cases
> We've had a great deal of experience in this laboratory constructing viruses with
> various mutations, and none have ever been more virulent; most are attenuated.
> The same applies for research done in other laboratories. We have little clue how
> to make a more virulent virus.
but there are many papers demonstrating just this increase of virulence.
I don't know much outside influenza, but especially with reassorting influenza viruses :
we have 256 possible children, some are usually
more virulent than the parents, some are less virulent. Only ~10% do survive and replicate
and most transmit worse than in nature. But now I feel that we are getting close to successfully
create/detect and filter the potential candidates. We are clearly better than nature here,
which requires a (rare in humans) double-infection and competition (through immunity) with other viruses,
while we can learn and design and select to specifically target and optimize the outcome.
Since above study is not public and already starts with a HP-virus,
let me select this as an example instead, to demonstrate what I mean  Sun et.al., 2011:
[ For an overview of other reassortment studies see
[url]http://www.flutrackers.com/forum/showthread.php?t=203696[/url] ]
While most (46 out of 127) [H9N2+pH1N1)-reassortant viable children had lower pathogenicity
than the parents, there were still 8 out of 127 that had higher pathogenicity in mice than both
parents.Researchers and terrorists will learn how to create higher pathogenicity by reassortment
or passaging or combinations of both. And how to enhance it to ferrets,pigs,...,humans.
This was for reassortment experiments, but also for single mutations and passaging
there are many papers how these may increase virulence.
Some keywords that come to mind:: N66S in PB1-F2, E627K in PB2, H5N1 in mouse-brain
after passaging, chicken-adapted,quail-adapted H9N2, D225G in HA of pH1N1 and 1918-H1N1,
search "virulence mutations", "influenza"
> Part of the problem is that we focus on amino acid
> changes in isolation; in nature these are accompanied by hundreds of other changes
> which are eventually selected in various hosts to make the final pathogen.

in flu it's often just one mutation. And the mutations usually accumulate one by one.
Each of the viruses in that chain must be viable. We have many influenza sequences
meanwhile, so we can study the chains. And in the labs they can create these mutations
by passaging.

> We don't have a chance at duplicating this and I've never seen any laboratory come close.
Palese,Fouchier,Kawaka,...I feel they are pretty close
> Just take a look at the scientific literature on viral pathogenesis.
> My beliefs are indeed relevant. They are based on 30+ years of doing research in the
> laboratory on viral pathogenesis, and keeping up with the literature.
but things have changed a lot recently. Now we have reverse genetics, better organized
labs with rooms full of ferret-cages, 200000 flu sequences at genbank, 70000 flu-papers at pubmed.
Next Generation Sequencing


profvrr wrote:
> I firmly believe that laboratory-constructed viruses do not have what it
> takes to be a human pathogen: only viral evolution in nature can
> produce the right combination of RNA segments and mutations.
> ... I can find plenty of virologists who would have the same view.
> We are talking about humans, not animal models.
laboratory-constructed viruses do have what it takes to be a ferret pathogen ?
Humans are animals. We are not so special from the virus' POV.
Why might it work in different animals but not in humans ?
Presumably only because we can't test it in humans for ethical reasons.
There is no magical difference that separates humans from ferrets
but not ferrets from mice or guinea pigs. We cannot be 100% sure
before we tested it in humans - but maybe 80%, and that's still useful.
So lab-viruses probably often do have "what it takes to be an animal or
human pathogen" but tests to confirm this for humans are rarely available.


Thursday, May 2, 2013

H7N9 unlikely to go into mallards

let me repeat this, since I keep seeing concerns that
H7N9 may go into wild birds.

Avian influenza in wild birds, especially mallards (not geese,gulls,) mutates its proteins
in the inner segments only rarely. Flu is in mallards mainly
waterborne and infects in the intestine.
Only in poultry or mammals it then mutates more (protein,6 inner segments).
Such poultry mutated viruses are then after a few decades
no longer compatible for mallards and similar waterfowl, the main reservoir
for avian influenza..
The protein=amino-acid mutation counts in  H9N2 in the 6 inner segments went like this:

1980: 01,02,04,--,00,--,00,01 A/duck/Potsdam/15/1980(H7N7)
2001: 09,07,12,--,06,--,12,23 A/chicken/Shanghai/10/2001(H9N2)
2013: 07,13,19,--,09,--,27,34 A/China/2013(H7N9)

H9N2 in this form is in East China since around the late 1990s.
But even the H9N2 from 2001 above was no longer found in wild birds.
I assume this is mainly due to the many mutations in the segments 7 and 8,
which grew further to 27+34 now. You hardly find such viruses in mallards.
So a spread of H7N9 which has the same inner 6 segments as H9N2,
in wild birds, seems therefore unlikely.

some more counts:

distance from the bird index:


(edited 2013.05.02.12:00ET)

Wednesday, April 10, 2013


the new influenza strain "H7N9" that was first seen in Shanghai 2013
is likely a (46+123578)-reassortment of a waterfowl H7N9 virus and a local
poultry H9N2 virus.

The number of differences in the 8 segments to the best public
known matching poultryflu segments is:
(18+33+16+100+19+150+13+7) in the coding region of
(2282+2276+2153+1685+1499+1400+984+840)=13119 nucleotides,
with an estimated
nucleotide-differences from the next best available poultry matches
in the segments.

The number of differences in the 8 segments to the best public
known matching waterflu segments is:
(80+170+150+67+65+50+80+50) in the coding region of
(2282+2276+2153+1685+1499+1400+984+840)=13119 nucleotides,
with an estimated
difference from the next best available mallardlike matches in the segments.

That gives a (rough,+-20%) estimate for the MRCAD of novel H7N9 

with poultry H9N2 in the segments of

This will probaly go up when new related poultry H9N2 become available now. 
The best whole-virus match is
A/brambling/Beijing/16/2012/11/07(H9N2) with
(17,30,18,708,39,583,20,20) nucleotide differences
That brambling presumably got it from poultry.

This suggests a reassortment getting segments 4,6 from wild birds
(mallardlike) and segments 1,2,3,5,7,8 from poultry (H9N2)

In theory the 46-reassortment could have happened in 2006 and all
the other segments were acquired later by subsequent reassortments,
but that looks unlikely - how would it hide so long, why so many
reassortments? More likely that the common ancestor of the brambling
and H9N2 in 2011 was entirely H9N2.

The bigger mimimum distance in segments 4 and 6 could be explained
because more H9N2 poultry viruses than mallardflu H7N9 viruses
are available.

The (amino-) distance of the new H7N9 to the bird index
in the 8 segments is: (8,13,19,-,9,-,27,34).
This is already very non-mallardlike and away from the index.
I won't expect normal mallard-like waterfowl to catch such a virus.


Let's compare it with other strains.
Early H5N1, A/Ck/HK/YU22/2002 ("serotype Z") had (3,8,9,-,5,-,12,12)
differences from the index. It was in ducks (domestic and wild) and geese.
You can see how it "grows" already, especially in segments 7 and 8.
The original H5N1 outbreak in HK 1997 however was mainly a poultry
reassortant in the inner segments : A/HK/156/1997 (20,19,24,-,12,-,13,22) .
It was not prevalent in wild birds and they could wipe it out in poultry.
The reemerging H5N1 in 2002 then was more wildtype-like and
still circulates today.

Some other examples how flu goes from waterfowl into other species
and then starts to acquire amino  acid mutations in the inner segments:

H5N1,Vietnam 2004:(5,6,7,-,5,-,17,16)
H5N1,Cambodia 2012:(18,13,13,-,9,-,20,27)

human H1N1,USA 1918:(8,7,10,-,9,-,7,5)
human H3N2,USA 2007:(33,28,32,-,35,-,28,37)

equine H3N8,1963:(8,12,14,55,15,63,1,10)
equine H3N8,2008:(18,27,40,75,29,75,10,30)

Tuesday, April 9, 2013

influenza genetical evolution basics


genetic evolution of influenza
(some of these things are being simplified for an easier understanding)

Influenza A has 8 segments with a total of 13300 nucleotides from {A,C,G,T}
groups of 3 nucleotides (64 combinations) form one of 21 amino acids,
so changes in nucleotides not necessarily change the amino acid.
Changes in amino acids ("nonsynonymous") are much more important for the
properties of the virus than changes in nucleotides that keep the same
amino acids ("synonymous").

In this simplified model each nucleotide changes (mutates)
with probability 0.0025 per year and 80% of mutations are synonymous.
So from the number X of nucleotide differences in 2 influenza-A viruses
with Y commonly available nucleotides in the alignment
you can calculate an estimate of the date of the most recent common ancestor
(MRCAD) by the formular 
where D_i is the isolation date of virus i  (for evolution over small periods
of ~<20 years, else use the formula:
The diversity in the 8 segments is different.
Segments 1,2,3,5,7 all go back to a common ancester
~200 years ago. Segment 4 is usually subdivided into 16
subtypes, segment 6 into 9 and segment 8 into 2.
(ignoring flu in bats). Let's assume for simplicity that
each of these subtypes in segments 4,6,8
has also a common ancestor ~200 years ago like.
And that the common ancestor of 2 different subtypes (16,9,or 2)
in the same segment is ~400 years ago.
The usual name of the subtypes is by the enumeration of
segment 4 (HA) and segment 6 (NA) while segment 8 is being
ignored, in mammals and poultry it's almost always the same
(81), while in wild birds 82 occurs with frequency ~20%
and 81 with ~80%
The nucleotide mutation-rate in segments 4 and 6 is ~50% higher and
the amino-acid mutation rate (nonsynonymous) is ~100% higher
as in the other segments.

In addition to the mutations at nucleotides there is the
possibility that entire segments are shuffled ("reassortment"),
when two different influenza-A viruses enter the same cell.
Of course you need one of each of the segments for a working
new virus, so there are 256 possibilities to form a new combination.
Some of these are more likely than others, e.g. segments 2,4,6
should "fit" to one another and are less likely separated
in the shuffling. Let's say ~half as likely.

The typical hosts for influenza A are birds,humans,swine,horses.
Let's consider birds and humans here.
The base reservoir are waterfowl : mallards,pintails,teals,
shorebirds. Not geese,domestic ducks,gulls,
(for simplicity called waterfowl below)

In these we see reassortments of different viruses more often than
in other species, i.e. switching of segments 4 and 6
is more common. In addition to this in the inner segments
(1,2,3,5,7,8) nonsynonymous mutations are rarer and in fact
at the amino-acid level mallardflu inner segments all cluster
around one index-strain (or avian consensus) from which they
usually only move away 5-10 amino-acid differences.
This is not the case in segments 4,6 nor in the inner segments
of poultry or mammalean flu, where they move steadily away from
the index with rate ~0.005 per year.
So, that's how you can usually see whether an inner segment
is mallardflu or poultry or mammalean.
There is one other distinction and that is the proportion
of A or T nucleotides, which grows after prolonged time of
evolution (decades) in mammals at rate ~

There is (currently) no separate evolution of influenza-A in poultry
or mammals. They occasionally catch a new flu-A virus from waterfowl
this evolves for a while outside waterfowl until a new strain
is introduced and co-circulates or replaces the old one.
Thus the oldest current segments outside waterfowl are
the human segments that go back to the pandemic 1918.
horse-H7N7 probably extinct since the 1980s
South America

While human influenza goes around the world each year,
avian and swine influenza usually stay in their
continental block (NA,SA,EuAsOzAf) for years and decades
without widespread occurrance in the other blocks.
For WFF that means that in the inner segments we
have NA and EA variants that differ much in the
nucleotides but few in anino acids

to do:


Nonhuman influenza


list of substrains
events of avian-->mammal,poultry

distances between subtypes , big 180*180 table

additions, improvement suggestions are welcome


next:  H7N9(2013)


open letter to the influanza-A virus

dear influenza A virus,

we humans don't like you. You infect us and give us disease.
I know, this is not your purpose, it's just accidental.
You want to spread and replicate and evolve, OK, but it would be
best for humans and flu if you would do that asymptotically.
As you usually do it in waterfowl. Well, H5N1 was another
one of your "accidents" ...
Maybe you are not really interested in humans or other
mammals or poultry at all, your main playing ground are wild birds.
So let's make a deal, we help you to spread and evolve and you stop
giving us symptoms, OK ?
You know, we humans are very clever, we can grow food, eat it
and transform it easily into the material that you need to replicate.
In great masses. We can easily produce zillions of your kind this way
with little cost. If only you don't disturb us with infectikng all these
tissues and cells and giving us symptoms.
Most of these cell-attacks aren't really needed to spread, right ?
So please stop infecting them, while we would stop to attack
you with immunity and vaccines and antivirals.
And help you to travel the continents so you can mutate and reassort
all you want. As long as you don't make us sick or kill our birds.

See rhinovirus as an example. It infects us even more often than you do.
It did evolve into many different strains
It spreads respiratory as you. It still causes symptoms, but not so much.
This can still be improved ...

Ideally we would create some cells just for you, useless for us,
where you can replicate and spread.
We hope, that you will communicate with our immune system and alert us
when other evil pathogens enter to compete with your replicate-cells
and cause us symptoms and disease.
Just to our both benefit. And there's really no need to invite pneumonia,
that doesn't serve any of us.
So, do we have a deal ?

Well, I know, you won't read this, you are too stupid to read.
Most experts even think that you are not living at all.