1918 again? – Part 3

My most recent two blogs have described the remarkable similarities between the HA protein in the 1918 pandemic flu virus and the 2009 pandemic flu virus. However, it is important to note that this similarity is not due to a general sequence similarity. Indeed, an alignment of the HA proteins from A/South Carolina/1/18 (H1N1) and A/California/04/2009(H1N1) reveal an identity of only 86%, quite low. And yet, figure 3C from the Xu et al paper reveals that:

Antibody 2D1 exhibits strong binding to both 1918 HA and CA04 HA, but not to PR8 and HAs of other influenza subtypes, as tested in ELISA assay.

How to explain the remarkable ability of an antibody from over 90 years ago to specifically recognise another pandemic strain of influenza, but not more recent flu viruses? Physically, this may be due a similar epitope, a short segment of the protein, that is nearly identical between the two viruses. The three dimensional shapes of the HA proteins of the two viruses are also very similar, even though most of the primary sequence is quite different. Although this explains why the 2D1 antibody can recognise both viruses, it does not explain why the two viruses are so similar in this one specific way.

To address this question, we should start without preconceptions. This means that we should not assume that the virus evolved naturally or that it was made in a laboratory. Let us consider each of these possibilities to examine which is more likely. We will, of course, be speculating as there is no evidence that has been presented that conclusively proves either hypothesis.

If the remarkable similarity in 2D1 binding of the 1918 and 2009 pandemic strains was the result of natural processes, I can imagine two possible mechanisms. First, an extremely important epitope (short segment of amino acids) that bound to 2D1, was preserved, by sheer chance, over 90 years and just happened to end up in the 2009 pandemic virus. This seems highly unlikely to me, but was suggested in one of the speculative commentaries on these papers. A second possibility is that the epitope in question was under intense selection. That is, it conferred a very strong benefit to the viruses that carried it. However, this advantage would have to have been in animals that were infected with the virus, most likely pigs, because the same epitopes were not found in human viruses. This advantage would have had to have applied to pig viruses, but not to human viruses, until 2009, when it suddenly appeared in the pandemic 2009 virus, apparently without causing any loss of fitness in this particular human virus. This is possible, but not proven.

The other general possibility, that the virus was produced in a laboratory, is almost never discussed in scientific papers, but should be considered in light of the unusual properties of this virus, imo. How would one explain the low general similarity between the 1918 virus and the 2009 virus but high similarity with respect to 2D1 binding if one posits a lab origin? Rather directly, as it turns out. There is a laboratory technique know as immunoprecipitation. It involves using antibodies to specific epitopes to “pull out” particular proteins. One can imagine someone using an antibody to the 1918 virus to screen a large panel of constructed viruses for strains that resemble the 1918 virus in biology, but not general sequence. If this hypothesis is correct, then the ability of 2D1 to recognise the 2009 pandemic virus is not a coincidence – it is how this virus was selected. This is possible, but not proven.

Which general mechanism, an odd and never-before observed pattern of viral evolution or a laboratory immunoprecipitation assay is the more likely possibility? It is difficult to say, at this point. Perhaps further experiments will provide stronger evidence in favor of a natural evolution of this virus. However, at this time, the mounting number of odd features of the 2009 pandemic flu virus should give open-minded people cause for concern, imo.


Xu et al. (2010) Structural Basis of Preexisting Immunity to the 2009 H1N1 Pandemic Influenza Virus. Science.

Wei et al. (2010) Cross -Neutralization of 1918 and 2009 Influenza Viruses: Role of Glycans in Viral Evolution and Vaccine Design. Science Translational Medicine.

Itoh, et al. (2009) In vitro and in vivo characterization of new swine-origin H1N1 influenza viruses. Nature.

Settembre et al. (2010) H1N1: Can a Pandemic Cycle Be Broken? Science Translational Medicine.


7 thoughts on “1918 again? – Part 3

  1. I have a couple of questions. If H1N1 is a triple reassortant, are the genes donated from each reassortment source faithfully conserved from their donor? Or are there significant genetic differences within each gene segment from the donor source virus?

    There is a lot of emerging evidence that this virus is novel to pigs too – and not much it had been circulating within pigs in its current form prior to its emergence in humans last spring.

    If you recall, back in 2008 China had extensive outbreaks of PPRS and other fatal pig pathogens, such that China had to import livestock from the US and other countries to repopulate its pig farms. Is it possible that if any of the imported livestock were carrying flu viruses, that this could have been a mechanism by which European, US and Asian swine viruses could have met and exchanged such genetic material?


    Is there any evidence that Mexico or the US (or anywhere else for that matter) had been importing livestock from China and Europe to populate its pig farms to allow such a meeting of source viruses?

    If the individual source genes were relatively unchanged, couldn’t such a situation potentially explain a natural evolution within pigs in this manner, but quite possibly with a human as the final mixing vessel – or another animal?

    Can we show that this is implausible or possible on the basis of what we currently know?

    If the answer is no, then it raises questions as to a lab or other origin – but until we can rule this out as a possibility, it still remains the most probable explanation IMHO.

  2. Vibrant62, these are excellent questions.

    The donors for each of the genes have never been identified. Indeed, even determining what species of animal was last infected with a virus containing each gene is difficult to do due to the very low level of similarity. Try BLASTing each gene segment separately. See what you find. The last time I did this, some months ago, the best I could do was to say this gene has its closest match a virus that was in a bird, human or pig. But none of these matches were very good. Hence, I do not regard it as proven that the virus came pigs. This is an hypothesis with insufficient evidence, imo.

    It is possible that the true donor exists in pigs in a country with a poor record of surveillance, like China. Conceivably, one of these pigs could have been exported to the US or Mexico. However, we would have to assume that the virus was in pigs in China for many years but never crossed to humans. But when the pigs came over to the US or Mexico, the virus quickly jumped the species barrier and started infecting people. This is possible, but remains without evidence.

    None of the naturally occurring hypotheses that have been presented seem likely to me, although I confess they are possible. A lab based origin would explain many anomalies quite nicely. I realise that many suggest that the burden of proof is on those who would suggest a lab origin. But why is this so? Certainly, anyone who is aware of what is possible knows that this virus *could* have been made in the lab. We know that there are a number of anomalies with this virus that cannot easily be explained with a natural origin. Yet, the possibility of an unnatural origin is rarely discussed. To me, this is makes no scientific sense. If we are going to speculate wildly about a natural origin and derive fantasy phylogenies, we ought to at least mention the possibility of laboratory origin. I would suggest that we don’t for psychological and political reasons.

  3. Thanks for your answer. We do not appear to screen vermin in areas surrounding pig farms routinely to see if they carry influenza virus. Given that we routinely infect these animals in the course of experimentation, why do we seem to believe that they are incapable of natural infection? It would seem to me to be a potential natural source of mammalian influenza adaptation to rule out, yet there is no monitoring ongoing of this type I have been able to find. Vermin exist in high denisty in all areas, and especially around farming areas, and pig farms in particular.

    Using the sherlock homes analaogy, I am seeking to rule out all other possibilities before considering a man made option seriously – I just dont believe we know enough about influenza genetics to have been that clever..

  4. Vibrant62, I certainly agree that we do not screen enough animals, especially mammals, for influenza. Some years ago, I wrote a series of blogs about this with respect to H5N1:


    However, again, I do not agree that the burden of proof should logically fall on those who suggest the virus may have originated in a laboratory. We definitely do know enough to make educated guesses about what various combinations of flu genes might do. Further, one can use automated systems to screen for particular biological properties and test the final results in animals before releasing on the human population. If we do not seriously consider this possibility and discuss it openly, then we extend an invitation to bioweaponeers to push ahead with their plans as they will feel that they can create such monsters without fear of punishment. The precautionary principle should apply to bioweapons, just as it does to the other aspects of public health, imo.

    Note, I’m not saying that we should automatically assume that every outbreak of every virus is a bioweapons attack, only that this is one of the possibilities that should be considered as we work through the list of possibilities to find the most likely explanation.

  5. An intersting paper, that certainly throws the issues as to origins wide open. Balb/C mice are affected, but are wild type mice?

    One could argue that this paper provides support for non-porcine evolution on the one hand in wild mice, or lab development of the strain using these experimental mice on the other, especially if wild mice are not naturally affected.

    Clearly capture and testing of mice in the wild is necessary to see if these rodents are naturally part of the evolutionary chain of influenza development.

    Virus Res. 2010 Apr 7. [Epub ahead of print]
    Challenge and polymorphism analysis of the novel A (H1N1) influenza virus to normal animals.

    Linlin B, Lili X, Lingjun Z, Wei D, Hua Z, Hong G, Huihui S, Chunmei M, Qi L, Fengdi L, Honglin C, Lianfeng Z, Chuan Q.

    Pathogen experimental research center; Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Pan Jia Yuan Nan Li No.5, Chao Yang District, Beijing 100021, China.

    The novel influenza A (H1N1) virus that emerged from April 2009 in Mexico has spread rapidly to many countries and initiated a human pandemic. It is important to determine whether the virus has existed in, or will spread to, normal household animals, and whether A (H1N1) like viruses derived from the animal is able to proliferate in cell lines derived from human. In this current paper, familiar animals, including pigs, chickens, ducks, cats, dogs, rats, mice, and Brandt’s voles were challenged with the novel influenza A (H1N1) virus, and genetic variations of the viral genome were analyzed after three passages in the susceptible animals. To further determine the virulence of these animals derived influenza A (H1N1) -like viruses, viral replication dynamic curves were monitored after inoculation in MDCK cells and human A549 cells. Our results indicated that pigs, BALB/c mice, and Brandt’s voles, but not chickens, ducks, cats, dogs, and rats, could be infected by the novel influenza A (H1N1) virus. Genome sequence alignment results showed that there was one genetic variation (G408T) in the HA gene of Brandt’s vole derived virus and another one (C194A) in the NA gene of BALB/c mice derived virus, and the virulence of these two viruses in MDCK and A549 cells was significantly lower than the virus originally derived from human beings. Copyright © 2010. Published by Elsevier B.V.

    PMID: 20381552 [PubMed – as supplied by publisher]


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