Monday, July 02, 2012

The saga of Hush Bush continues..

Hello audience,

        Its not long ago since i had blogged about "Influenza lab created virus", that set stage for historical debate of the year in Science community. I dont know if i should call this post a follow up or just just yet another insight to the whole issue. Anyways, if you have not read my previous post on influenza A/H5N1 transmissibility, i recommend you first read the post (Link) and then get back to this page.

Photo 1: Avian Influenza virus

Photo 2: Dr Ron Fouchier

       Also i have a couple of links to some shows that i recommend you watch or listen to before going ahead. The first is the meeting held by NSABB (Link) that discussed on the publication of the paper, and the second is a podcast by TWiV 182 (Link). These episodes should give you a complete picture of how the story has twisted and turned in the last few months. And ultimately when the paper published, the most important point that was taken home was "Only 5 mutations are crucial for an avian influenza of H5N1 to cross species barrier and invade the human territorial lines". And suddenly there was a hush bush created. For people who are still in doubt about the risks and benifits of influenza research you must read a the science paper in June 2012 issue by Anthony S. Fauci and Francis S. Collins (Link)

      Thats the recap of the story (If i could call it so). As the legend goes, hot science stories never crumble to an end quickly. And here it makes the news again (Don't get me wrong on this. I just mean to dramatise, to say that there's more insight into the story of Influenza A H5/N1 transmissibility).

      So with all the links, and all the background let me dive into the topic. The paper in discussion, in this blogpost is a paper by Colin A. Russell etal titled "The Potential for Respiratory Droplet–Transmissible A/H5N1 Influenza Virus to Evolve in a Mammalian Host".

      The paper starts with a statement that says it all "A/Indonesia/5/2005 avian A/H5N1 influenza virus may require as few as five amino acid substitutions, and the A/Vietnam/1203/2004 A/H5N1 influenza virus requires four substitutions and reassortment to become transmissible between ferrets via respiratory droplets". The leucine at 222 and serine at 224 in the hemagglutinin (HA) is known to provide human like alpha-2-6–linked sialic acid.

         Ok, So what has been done in this study is to look at various sequences of Influenza A H5N1 virus collected over the time and, circled out the ones that comes close to the required amino acid substitutions. Now, here's the catch. Many viruses that might have evolved with this change in birds will be simply negatively selected, because they are still in birds. So thats why probably they haven't made into humans in a notifiable bang as of yet. The second most important point that struck me hard is the data of samples from Nepal, Mongolia, Japan, and Korea (Time period 2009-11), belonging to the clade They were the closest ones.Of the 94 strains they have sequenced 17, but none yielded a E627K substitution. E627K substitution is connected with mammalian polymerase adaptation. To me that makes sense again, because they are still in birds. Colin Russell, said: “Viruses that have two of these mutations are already common in birds, meaning that there are viruses that might have to acquire only three additional mutations in a human to become airborne transmissible. The next key question is ‘is three a lot, or a little?’"

          Let me digress a bit here. I was curious to know if the H5N1 has already made big news anywhere. So i fished out the WHO data (Link). And I didn't find Nepal, Mongolia, Japan or Korea in the list where cases of humans were reported. Indonesia was leading reported area. A total of 606 cases were confirmed with 357 deaths. Thats aprox 58.91%! So now i see the source why people think H5N1 is fatal. The fact is that the 606 are cases of known apparent infection. The asymptomatic ones is not accounted for denominator in this case. Fig 1 is a study by Smith etal, which was looking for predominance of  H5N1 influenza variant in China. They were able to isolate a good number of them, but their serological conversion was not so good. 

Fig 1: Comparison of H5N1 influenza virus isolation rate (%) in chicken (A), duck (B) and goose (C) from southern China, July 2004 to June 2006. (Source)

Smith etal also made a clear statement in the paper, "The predominance of this virus over a large geographical region within a short period directly challenges current disease control measures." The highlighted region says it all. But they were mainly looking for viruses not its sequences.

So back to the paper what we i was blabbing about. The authors go on to make a note that surveillance has detected humans with A/H5N1 viruses four nucleotide mutations and three mutations away in HA. "So if the species barrier jump is possible for this virus?", that was their question. This gets me to lit bit of confusion here. H5N1 infections are reported (See WHO link above). So instead of going into the mathematical model, i would have tried looking into the sequences of the viruses that already has caused infection and then see are they the same that "Ron Fouchier" had projected for ferrets (Either i haven't caught hold of some point or this angle of looking has flaws!! I don't know, or rarely maybe am absolutely right).

Fig 2: Documented Avian Influenza infections in humans (Click here for source)

So with a mathematical model approach (At this point am doomed. Am so bad with math u see, and i just believe what they are saying here). And the fig 3 is what they came up with after considering random mutation, positive selection and long infection.

Fig 3: Expected absolute numbers and proportions of respiratory droplet–transmissible A/H5N1 virions within a host initially infected by strains that require five (blue), four (green), three (orange), two (red), or one (purple) mutation (or mutations) to become respiratory droplet–transmissible.

So they concluded that the factors that may play major contributions, positively for gaining those important mutations include Random mutation (Any given virus has enough of those), Positive selection, Long infection, Functionally equivalent substitutions (Given that virus is good at mutations selection pressure should ease this factor)Diversity in the within-bird virus population and Transmission also accounts. The factors likely to negatively regulate were an effective immune response, Deleterious substitutions and order of acquiring those mutations. (Additional Source).

Derek Smith had to say about this "With the information we have, it is impossible to say what the exact risk is of the virus becoming airborne transmissible among humans. However, the results suggest that the remaining three mutations could evolve in a single human host, making a virus evolving in nature a potentially serious threat".

So, if you had asked me, my views are so. First, the paper makes an attempt to answer the question "If its possible?". But just as any other biological property the percentage of chance is very unpredictable. Second, the paper should have gathered more sequences. They have studied only 18% of mutations and say E627K substitution was not detected. And if that could have come from the sequence of the ones who were in the clinic it would have been a strong proof. (Maybe they will do it in future. Am not a flu virologist, but that data would impress me). But then the paper do suggest that possibility is not nil. As Prof Smith puts it "The situation is similar to assessing the risk of an earthquake or tsunami". So guess we need to have something like we have for earthquake or tsunami. Probably stock pile some vaccine.
Colin A. Russell, Judith M. Fonville, AndrĂ© E. X. Brown, David F. Burke, David L. Smith, Sarah L. James, Sander Herfst, Sander van Boheemen, Martin Linster, Eefje J. Schrauwen, Leah Katzelnick, Ana MosterĂ­n, Thijs Kuiken, Eileen Maher, Gabriele Neumann, Albert D. M. E. Osterhaus, Yoshihiro Kawaoka, Ron A. M. Fouchier, & Derek J. Smith (2012). The Potential for Respiratory Droplet–Transmissible A/H5N1 Influenza Virus to Evolve in a Mammalian Host Science (New York, N.Y.) : 10.1126/science.1222526

Further reading:

1. Influenza Hush Bush, Link

2. Anthony S. Fauci and Francis S. Collins. Benefits and Risks of Influenza Research: Lessons Learned. Science 22 June 2012: Vol. 336 no. 6088 pp. 1522-1523. Link

3. Bruce Alberts, H5N1. Science 22 June 2012: Vol. 336 no. 6088 p. 1521. Link

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