tag:blogger.com,1999:blog-795645819591830262024-03-13T04:37:48.563-07:00flugsgshttp://www.blogger.com/profile/02467330946443442615noreply@blogger.comBlogger5125tag:blogger.com,1999:blog-79564581959183026.post-60448119578808459172013-05-14T00:45:00.000-07:002013-05-14T06:10:07.841-07:00man-made pandemics<div>
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[ discussion from <br /><a href="http://www.virology.ws/2013/05/07/influenza-h5n1-x-h1n1-reassortants-ignore-the-headlines-its-good-science/">http://www.virology.ws/2013/05/07/influenza-h5n1-x-h1n1-reassortants-ignore-the-headlines-its-good-science/</a> ]<br />[ I also put it here :<br /><a href="http://gsgs2.blogspot.de/2013/05/man-made-pandemics.html">http://gsgs2.blogspot.de/2013/05/man-made-pandemics.html</a><br />and here:<br /><a href="http://www.flutrackers.com/forum/showpost.php?p=497438">http://www.flutrackers.com/forum/showpost.php?p=497438</a></div>
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profvrr wrote on 2013.May.13 in response to DavidS</div>
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> Animal models are not predictors of what will happen in humans. <br /><br />somehow they are.That's why we are using them, why you say "it's good science" <br />You probably meant: are not so good predictors (as most think)</div>
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> We study infections in animals to obtain mechanistic clues; </div>
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you say mechanistic clues, I'd say probability estimates</div>
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> conclusions about what happens in people require further testing. There are dozens <br />> of examples of this in the literature. Drugs and vaccines are tested in several animal models, <br />> but are the drugs and vaccines then released for humans? Of course not; clinical <br />> trials are done. </div>
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which often however confirm the animal tests. I'd guess in ~70% of cases</div>
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> We've had a great deal of experience in this laboratory constructing viruses with <br />> various mutations, and none have ever been more virulent; most are attenuated. <br />> The same applies for research done in other laboratories. We have little clue how <br />> to make a more virulent virus. </div>
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but there are many papers demonstrating just this increase of virulence.<br />I don't know much outside influenza, but especially with reassorting influenza viruses : <br />we have 256 possible children, some are usually <br />more virulent than the parents, some are less virulent. Only ~10% do survive and replicate<br />and most transmit worse than in nature. But now I feel that we are getting close to successfully<br />create/detect and filter the potential candidates. We are clearly better than nature here,<br />which requires a (rare in humans) double-infection and competition (through immunity) with other viruses,<br />while we can learn and design and select to specifically target and optimize the outcome.<br />Since above study is not public and already starts with a HP-virus,<br />let me select this as an example instead, to demonstrate what I mean Sun et.al., 2011: <br />[url]http://www.pnas.org/content/early/2011/02/23/1019109108[/url]<br />[ For an overview of other reassortment studies see<br />[url]http://www.flutrackers.com/forum/showthread.php?t=203696[/url] ]<br />While most (46 out of 127) [H9N2+pH1N1)-reassortant viable children had lower pathogenicity <br />than the parents, there were still 8 out of 127 that had higher pathogenicity in mice than both <br />parents.Researchers and terrorists will learn how to create higher pathogenicity by reassortment<br />or passaging or combinations of both. And how to enhance it to ferrets,pigs,...,humans.</div>
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This was for reassortment experiments, but also for single mutations and passaging<br />there are many papers how these may increase virulence.<br />Some keywords that come to mind:: N66S in PB1-F2, E627K in PB2, H5N1 in mouse-brain <br />after passaging, chicken-adapted,quail-adapted H9N2, D225G in HA of pH1N1 and 1918-H1N1,<br />search "virulence mutations", "influenza"</div>
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<a href="http://www.nature.com/nrmicro/journal/v9/n8/fig_tab/nrmicro2613_T1.html">http://www.nature.com/nrmicro/journal/v9/n8/fig_tab/nrmicro2613_T1.html</a></div>
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> Part of the problem is that we focus on amino acid <br />> changes in isolation; in nature these are accompanied by hundreds of other changes <br />> which are eventually selected in various hosts to make the final pathogen. <br /><br />in flu it's often just one mutation. And the mutations usually accumulate one by one.<br />Each of the viruses in that chain must be viable. We have many influenza sequences<br />meanwhile, so we can study the chains. And in the labs they can create these mutations<br />by passaging.<br /><br />> We don't have a chance at duplicating this and I've never seen any laboratory come close. </div>
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Palese,Fouchier,Kawaka,...I feel they are pretty close</div>
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> Just take a look at the scientific literature on viral pathogenesis.<br />> My beliefs are indeed relevant. They are based on 30+ years of doing research in the <br />> laboratory on viral pathogenesis, and keeping up with the literature.</div>
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but things have changed a lot recently. Now we have reverse genetics, better organized<br />labs with rooms full of ferret-cages, 200000 flu sequences at genbank, 70000 flu-papers at pubmed.<br />Next Generation Sequencing</div>
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<br />profvrr wrote:<br />> I firmly believe that laboratory-constructed viruses do not have what it <br />> takes to be a human pathogen: only viral evolution in nature can <br />> produce the right combination of RNA segments and mutations. <br />> ... I can find plenty of virologists who would have the same view. <br />> We are talking about humans, not animal models.</div>
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laboratory-constructed viruses do have what it takes to be a ferret pathogen ?<br />Humans are animals. We are not so special from the virus' POV.<br />Why might it work in different animals but not in humans ?<br />Presumably only because we can't test it in humans for ethical reasons.<br />There is no magical difference that separates humans from ferrets<br />but not ferrets from mice or guinea pigs. We cannot be 100% sure<br />before we tested it in humans - but maybe 80%, and that's still useful.<br />So lab-viruses probably often do have "what it takes to be an animal or <br />human pathogen" but tests to confirm this for humans are rarely available.</div>
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gsgshttp://www.blogger.com/profile/02467330946443442615noreply@blogger.com0tag:blogger.com,1999:blog-79564581959183026.post-80039739152118318302013-05-02T08:44:00.000-07:002013-05-02T09:07:09.194-07:00H7N9 unlikely to go into mallards<div>
let me repeat this, since I keep seeing concerns that<br />
H7N9 may go into wild birds.<br />
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Avian influenza in wild birds, especially mallards (not geese,gulls,) mutates its proteins<br />
in the inner segments only rarely. Flu is in mallards mainly<br />
waterborne and infects in the intestine.<br />
Only in poultry or mammals it then mutates more (protein,6 inner segments).<br />
Such poultry mutated viruses are then after a few decades<br />
no longer compatible for mallards and similar waterfowl, the main reservoir<br />
for avian influenza..<br />
The protein=amino-acid mutation counts in H9N2 in the 6 inner segments went like this:<br />
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1980: 01,02,04,--,00,--,00,01 A/duck/Potsdam/15/1980(H7N7)<br />
2001: 09,07,12,--,06,--,12,23 A/chicken/Shanghai/10/2001(H9N2)<br />
2013: 07,13,19,--,09,--,27,34 A/China/2013(H7N9)<br />
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H9N2 in this form is in East China since around the late 1990s.<br />
But even the H9N2 from 2001 above was no longer found in wild birds.</div>
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I assume this is mainly due to the many mutations in the segments 7 and 8,</div>
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which grew further to 27+34 now. You hardly find such viruses in mallards.<br />
So a spread of H7N9 which has the same inner 6 segments as H9N2,</div>
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in wild birds, seems therefore unlikely.</div>
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some more counts:<br />
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distance from the bird index:<br />
OR:7,4,7,-,2,-,1,2<br />
CA:8,5,8,-,4,-,3,6<br />
QA:10,4,7,-,2,-,3,6<br />
98:8,6,11,-,4,-,15,23<br />
00:6,4,9,-,5,-,12,21<br />
01:9,7,12,-,6,-,12,23<br />
09:5,12,16,-,10,-,27,31<br />
13:7,13,19,-,9,-,27,34<br />
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OR:A/Duck/HK/702/1979(H9N2)<br />
QA:A/Duck/HK/702/1979-quail-adapted(H9N2)<br />
CA:A/Duck/HK/702/1979-chicken-adapted(H9N2)<br />
98:A/Chicken/Shanghai/F/1998(H9N2)<br />
00:A/Chicken/Shanghai/3/2000(H9N2)<br />
01:A/Chicken/Shanghai/10/2001(H9N2)<br />
13:A/Index/2013(H7N9)<br />
09:A/Index/poultry/East-China/2009(H9N2)<br />
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(edited 2013.05.02.12:00ET)<br />
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gsgshttp://www.blogger.com/profile/02467330946443442615noreply@blogger.com0tag:blogger.com,1999:blog-79564581959183026.post-55032565816790331072013-04-10T02:37:00.001-07:002013-04-12T03:48:11.155-07:00H7N9<br /><span style="font-family: Arial; font-size: x-small;">the new influenza strain "H7N9" that was first seen in Shanghai 2013<br />is likely a (46+123578)-reassortment of a waterfowl H7N9 virus and a local<br />poultry H9N2 virus.<br /><br />The number of differences in the 8 segments to the best public<br />known matching poultryflu segments is:<br />(18+33+16+100+19+150+13+7) in the coding region of<br />(2282+2276+2153+1685+1499+1400+984+840)=13119 nucleotides,<br />with an estimated<br />(0.79%,1.45%,0.74%,5.93%,1.27%,10.71%,1.32%,0.83%)<br />nucleotide-differences from the next best available poultry matches <br />in the segments.<br /><br />The number of differences in the 8 segments to the best public<br />known matching waterflu segments is:<br />(80+170+150+67+65+50+80+50) in the coding region of<br />(2282+2276+2153+1685+1499+1400+984+840)=13119 nucleotides,<br />with an estimated<br />(3.51%,7.47%,6.97%,3.98%,4.34%,3.57%,8.13%,5.95%)<br />difference from the next best available mallardlike matches in the segments.<br /><br />That gives a (rough,+-20%) estimate for the MRCAD of novel H7N9 </span><br />
<span style="font-family: Arial; font-size: x-small;">with poultry H9N2 in the segments of<br />(2011/06,2009/09,2011/05,2006/12,2009/02,2006/05,2009/08,2010/07)</span><br />
<span style="font-family: Arial; font-size: x-small;">This will probaly go up when new related poultry H9N2 become available now. </span><br />
<span style="font-family: Arial; font-size: x-small;">The best whole-virus match is <br />A/brambling/Beijing/16/2012/11/07(H9N2) with<br />(17,30,18,708,39,583,20,20) nucleotide differences<br />That brambling presumably got it from poultry.<br /><br />This suggests a reassortment getting segments 4,6 from wild birds <br />(mallardlike) and segments 1,2,3,5,7,8 from poultry (H9N2)<br /><br />In theory the 46-reassortment could have happened in 2006 and all<br />the other segments were acquired later by subsequent reassortments,<br />but that looks unlikely - how would it hide so long, why so many<br />reassortments? More likely that the common ancestor of the brambling<br />and H9N2 in 2011 was entirely H9N2.<br /><br />The bigger mimimum distance in segments 4 and 6 could be explained<br />because more H9N2 poultry viruses than mallardflu H7N9 viruses<br />are available. <br /><br />The (amino-) distance of the new H7N9 to the bird index <br />in the 8 segments is: (8,13,19,-,9,-,27,34).<br />This is already very non-mallardlike and away from the index.<br />I won't expect normal mallard-like waterfowl to catch such a virus.<br /><br />---------------------------------------------------<br /><br />Let's compare it with other strains.<br />Early H5N1, A/Ck/HK/YU22/2002 ("serotype Z") had (3,8,9,-,5,-,12,12)<br />differences from the index. It was in ducks (domestic and wild) and geese.<br />You can see how it "grows" already, especially in segments 7 and 8.<br />The original H5N1 outbreak in HK 1997 however was mainly a poultry <br />reassortant in the inner segments : A/HK/156/1997 (20,19,24,-,12,-,13,22) . <br />It was not prevalent in wild birds and they could wipe it out in poultry. <br />The reemerging H5N1 in 2002 then was more wildtype-like and <br />still circulates today.<br /><br />Some other examples how flu goes from waterfowl into other species<br />and then starts to acquire amino acid mutations in the inner segments:<br /><br />H5N1,Vietnam 2004:(5,6,7,-,5,-,17,16)<br />H5N1,Cambodia 2012:(18,13,13,-,9,-,20,27)<br /><br />human H1N1,USA 1918:(8,7,10,-,9,-,7,5)<br />human H3N2,USA 2007:(33,28,32,-,35,-,28,37)<br /><br />equine H3N8,1963:(8,12,14,55,15,63,1,10)<br />equine H3N8,2008:(18,27,40,75,29,75,10,30)<br /></span>gsgshttp://www.blogger.com/profile/02467330946443442615noreply@blogger.com6tag:blogger.com,1999:blog-79564581959183026.post-91695767454474244102013-04-09T10:46:00.000-07:002013-04-09T12:14:36.679-07:00influenza genetical evolution basics<span style="font-family: Arial; font-size: x-small;">--------------------</span><br />
<span style="font-family: Arial; font-size: x-small;">------draft--------</span><br />
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<span style="font-family: Arial; font-size: x-small;">genetic evolution of influenza<br />------------------------------<br />(some of these things are being simplified for an easier understanding)<br /><br />Influenza A has 8 segments with a total of 13300 nucleotides from {A,C,G,T}<br />groups of 3 nucleotides (64 combinations) form one of 21 amino acids,<br />so changes in nucleotides not necessarily change the amino acid.<br />Changes in amino acids ("nonsynonymous") are much more important for the <br />properties of the virus than changes in nucleotides that keep the same <br />amino acids ("synonymous").<br /><br />In this simplified model each nucleotide changes (mutates)<br />with probability 0.0025 per year and 80% of mutations are synonymous.<br />So from the number X of nucleotide differences in 2 influenza-A viruses</span><span style="font-family: Arial; font-size: x-small;">with Y commonly available nucleotides in the alignment</span><br />
<span style="font-family: Arial; font-size: x-small;">you can calculate an estimate of the date of the most recent common ancestor</span><br />
<span style="font-family: Arial; font-size: x-small;">(MRCAD) by the formular </span><br />
<span style="font-family: Arial; font-size: x-small;">where D_i is the isolation date of virus i (for evolution over small periods</span><br />
<span style="font-family: Arial; font-size: x-small;">of ~<20 years, else use the formula:</span><br />
<span style="font-family: Arial; font-size: x-small;">The diversity in the 8 segments is different.<br />Segments 1,2,3,5,7 all go back to a common ancester<br />~200 years ago. Segment 4 is usually subdivided into 16 <br />subtypes, segment 6 into 9 and segment 8 into 2.<br />(ignoring flu in bats). Let's assume for simplicity that<br />each of these subtypes in segments 4,6,8<br />has also a common ancestor ~200 years ago like.<br />And that the common ancestor of 2 different subtypes (16,9,or 2)<br />in the same segment is ~400 years ago.<br />The usual name of the subtypes is by the enumeration of <br />segment 4 (HA) and segment 6 (NA) while segment 8 is being<br />ignored, in mammals and poultry it's almost always the same<br />(81), while in wild birds 82 occurs with frequency ~20%<br />and 81 with ~80%<br />The nucleotide mutation-rate in segments 4 and 6 is ~50% higher and<br />the amino-acid mutation rate (nonsynonymous) is ~100% higher<br />as in the other segments.<br /><br />In addition to the mutations at nucleotides there is the<br />possibility that entire segments are shuffled ("reassortment"), <br />when two different influenza-A viruses enter the same cell.<br />Of course you need one of each of the segments for a working<br />new virus, so there are 256 possibilities to form a new combination.<br />Some of these are more likely than others, e.g. segments 2,4,6<br />should "fit" to one another and are less likely separated<br />in the shuffling. Let's say ~half as likely.<br /><br />The typical hosts for influenza A are birds,humans,swine,horses.<br />Let's consider birds and humans here.<br />The base reservoir are waterfowl : mallards,pintails,teals,<br />shorebirds. Not geese,domestic ducks,gulls,<br />(for simplicity called waterfowl below)<br /><br />In these we see reassortments of different viruses more often than <br />in other species, i.e. switching of segments 4 and 6<br />is more common. In addition to this in the inner segments<br />(1,2,3,5,7,8) nonsynonymous mutations are rarer and in fact<br />at the amino-acid level mallardflu inner segments all cluster<br />around one index-strain (or avian consensus) from which they<br />usually only move away 5-10 amino-acid differences.<br />This is not the case in segments 4,6 nor in the inner segments<br />of poultry or mammalean flu, where they move steadily away from<br />the index with rate ~0.005 per year.<br />So, that's how you can usually see whether an inner segment<br />is mallardflu or poultry or mammalean.<br />There is one other distinction and that is the proportion<br />of A or T nucleotides, which grows after prolonged time of<br />evolution (decades) in mammals at rate ~<br /><br />There is (currently) no separate evolution of influenza-A in poultry <br />or mammals. They occasionally catch a new flu-A virus from waterfowl<br />this evolves for a while outside waterfowl until a new strain<br />is introduced and co-circulates or replaces the old one.<br />Thus the oldest current segments outside waterfowl are<br />the human segments that go back to the pandemic 1918.<br />horse-H7N7 probably extinct since the 1980s<br />17g<br />South America<br /><br />While human influenza goes around the world each year,<br />avian and swine influenza usually stay in their<br />continental block (NA,SA,EuAsOzAf) for years and decades<br />without widespread occurrance in the other blocks.<br />For WFF that means that in the inner segments we<br />have NA and EA variants that differ much in the<br />nucleotides but few in anino acids</span><br />
<span style="font-family: Arial; font-size: x-small;">to do:</span><br />
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<span style="font-family: Arial; font-size: x-small;">clouds<br /><br />Nonhuman influenza<br /><br /><br /><br /><br />humans:H3N2,H1N1,H1N2,H7N7,H9N2<br />swine:<br />horses:<br />dogs:<br />poultry:<br />mallards:<br /><br />mrca<br />list of substrains<br />events of avian-->mammal,poultry</span><br />
<span style="font-family: Arial; font-size: x-small;">flugenome.org<br />distances between subtypes , big 180*180 table<br /><br /><br /><br /><br />additions, improvement suggestions are welcome<br /><br /><br /><br />---------------------------------------------<br /><br />next: H7N9(2013)<br /><br /><br />th</span>gsgshttp://www.blogger.com/profile/02467330946443442615noreply@blogger.com0tag:blogger.com,1999:blog-79564581959183026.post-19755993156457916812013-04-09T10:33:00.003-07:002013-04-09T10:33:59.416-07:00open letter to the influanza-A virus<span style="font-family: Arial; font-size: x-small;">dear influenza A virus,<br /><br />we humans don't like you. You infect us and give us disease.<br />I know, this is not your purpose, it's just accidental.<br />You want to spread and replicate and evolve, OK, but it would be<br />best for humans and flu if you would do that asymptotically.<br />As you usually do it in waterfowl. Well, H5N1 was another<br />one of your "accidents" ...<br />Maybe you are not really interested in humans or other <br />mammals or poultry at all, your main playing ground are wild birds.<br />So let's make a deal, we help you to spread and evolve and you stop<br />giving us symptoms, OK ?<br />You know, we humans are very clever, we can grow food, eat it<br />and transform it easily into the material that you need to replicate.<br />In great masses. We can easily produce zillions of your kind this way<br />with little cost. If only you don't disturb us with infectikng all these<br />tissues and cells and giving us symptoms.<br />Most of these cell-attacks aren't really needed to spread, right ?<br />So please stop infecting them, while we would stop to attack<br />you with immunity and vaccines and antivirals.<br />And help you to travel the continents so you can mutate and reassort<br />all you want. As long as you don't make us sick or kill our birds.<br /><br />See rhinovirus as an example. It infects us even more often than you do.<br />It did evolve into many different strains<br />It spreads respiratory as you. It still causes symptoms, but not so much.<br />This can still be improved ...<br /><br />Ideally we would create some cells just for you, useless for us, <br />where you can replicate and spread.<br />We hope, that you will communicate with our immune system and alert us<br />when other evil pathogens enter to compete with your replicate-cells<br />and cause us symptoms and disease.<br />Just to our both benefit. And there's really no need to invite pneumonia,<br />that doesn't serve any of us.<br />So, do we have a deal ?<br /><br />Well, I know, you won't read this, you are too stupid to read.<br />Most experts even think that you are not living at all.<br /><br /> </span>gsgshttp://www.blogger.com/profile/02467330946443442615noreply@blogger.com0