Influenza A/Mexico/2009 (H1N1): Absence of crucial virulence marker

2 May 2009

influenza-rna-2The second RNA segment of the influenza virus genome encodes two proteins, PB1 and PB1-F2.  The latter protein is believed to be an important determinant of virulence of influenza virus. Can we learn anything about the virulence of the new influenza virus H1N1 strains from a study of this protein?

During influenza virus infection, PB1-F2 is targeted to the mitochondria, where it induces a form of cell death known as apoptosis. Experiments in a mouse model of influenza virus infection have shown that PB1-F2 regulates lethality of the virus. By comparing the infection of mice with two strains of influenza virus, one of which produces much lower levels of the PB1-F2 protein, it was found that the protein enhances inflammation and increases frequency and severity of secondary bacterial pneumonia. A specific amino acid at position 66 of this protein appears to be an important determinant of viral virulence. This amino acid is a serine in the 1918 H1N1 influenza virus, in a 1997 avian H5N1 isolate from the Hong Kong outbreak, and in the H2N2 (1957) and H3N2 (1968) pandemic strains. Other less pathogenic influenza virus isolates have an asparagine at this position. Two viruses were constructed which differ at amino acid 66 of the PB1-F2 protein, and the virulence of these viruses was determined in mice. The influenza virus with a serine at amino acid 66 was pathogenic in mice, while the virus with an asparagine was significantly less virulent. Increased pathogenicity of the virulent virus was associated with higher levels of virus replication in the lungs. The results of these studies show that the PB1-F2 protein affects pathogenicity in a mouse model, and that position 66 plays an important role.

h1n1-pb2-f2

Truncated PB1-F2

Because the amino acid change N66S of PB1-F2 is present in the three previous pandemic influenza virus strains – 1918 H1N1, 1957 H2N2, and 1968 H3N2 – it would be of interest to determine which amino acid, N or S, is present in the new H1N1 influenza virus strain that is spreading globally. However, examination of the nucleotide sequence of RNA from the current H1N1 isolates shows that these viruses do not even produce a PB1-F2 protein – a stop codon is present after amino acid 11 (see figure). In fact, many other influenza virus strains do not produce the protein. While the PB1-F2 protein is not the only determinant of influenza virus virulence, we can at least eliminate any contribution of this viral protein to increased lethality. As Peter Palese has written in today’s Wall Street Journal, “If this virulence marker is necessary for an influenza virus to become highly pathogenic in humans or in chickens, then the current swine virus doesn’t have what it takes to become a major killer.”

Conenello, G., Zamarin, D., Perrone, L., Tumpey, T., & Palese, P. (2007). A Single Mutation in the PB1-F2 of H5N1 (HK/97) and 1918 Influenza A Viruses Contributes to Increased Virulence PLoS Pathogens, 3 (10) DOI: 10.1371/journal.ppat.0030141

MCAULEY, J., HORNUNG, F., BOYD, K., SMITH, A., MCKEON, R., BENNINK, J., YEWDELL, J., & MCCULLERS, J. (2007). Expression of the 1918 Influenza A Virus PB1-F2 Enhances the Pathogenesis of Viral and Secondary Bacterial Pneumonia Cell Host & Microbe, 2 (4), 240-249 DOI: 10.1016/j.chom.2007.09.001

  • http://www.virology.ca Chris Upton

    But what is needed to create a functional PB2-F2 gene?
    Single point mutation or new re-assorted virus?

  • http://www.virology.ws profvrr

    Excellent point…a single point mutation would remove the stop codon,
    and produce a PB2-F2 protein. You can see from the sequence that's all
    it would take. Of course, reassortment could also do it, but it's not
    necessary.

  • dave

    And if a single point mutation removes the stop codon, what do you see at position 66 and how do you think virulence will be affected?

  • Matt Dubuque

    How do we know this analysis applies to what has been afflicting the Mexican population?

    There has been no release of any Mexican sequences, as far as I know.

    Therefore, scientifically speaking, how is this different from anecdotal evidence?

    I'm not trying to be harsh, but isn't this speculative without this Mexican sequences from a purely objective, rational, scientific view?

  • Anonymous

    There is some information about Mexican isolates here:
    http://scienceblogs.com/digitalbio/2009/04/did_

    Nickel summary: those who have seen data from Mexico say the sequences are highly similar to what we have seen.

  • Matt Dubuque

    Thanks, but the issue is why the profound and protracted delay in posting the entire sequences publicly for the world to see? It's urgent and important and has already been done for several US isolates.

    Why the delay? There has simply been no satisfactory explanation.

  • M. A. Ramakrishnan

    Please correct as PB1-F2 (including text)

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  • nobody
  • nobody
  • ocohen

    the 1918 pandemic started in springtime as a mild disease, fizzled over the summer, and started killing with a vengeance in the fall. Are there any data to suggest that the early strain lacked the PB1-F2 signature and then acquired it by mutation by the time it re-emerged in the fall? Presumably the reconstructed 1918 sequences from victims buried in permafrost are from after the fall of 1918?

  • http://www.virology.ws profvrr

    The sequences of many Mexican isolates have now been released at
    GISAID – Global Initiative on Sharing Avian Influenza Data.
    Registration is required to access the data. I do not understand why
    the sequences were released here and not at NCBI.

    I'll be looking at these sequences today with respect to the PB1-F2 question.

  • http://www.virology.ws profvrr

    You would have to remove the first stop codon and a second as well
    downstream. Then position 66 would be an asparagine, which is found in
    the less virulent strains.

  • http://www.virology.ws profvrr

    Yes, the 1918 isolates were from September-November 1918. So we cannot
    answer your good question, unless earlier specimens turn up.

  • giuseppe

    looking at pb1-f2 gene of h1n1 2009 i see:
    (nucleotide position are referred to this sample from ncbi database: FJ998226 (A/Mexico/InDRE4487/2009(H1N1)))
    start codon at position 105..107 (on a different frame from pb1 gene, starting at position 11..13)
    first stop codon, at position 138..140 (after 11th codon)
    a second stop codon at position 276..278 (after 57th codon)
    and another stop codon at position 366..368 (after 87th codon)
    according to this http://findarticles.com/p/articles/mi_m0GVK/is_
    at least a 78 a.a. polypeptide is needed to have a functional pb1-f2 protein, so should be required two base mutations:
    139 A=>T and 277 A=>G
    so my question is: is it possible to estimate the probability that this mutations occurs?
    (are there any data on influenza A mutation rate for this gene or locus?)

  • http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http://tree.bio.ed.ac.uk/groups/influenza Brian Foley

    The sequence you were looking at, is not the only one to have no functional PB1-F2 reading frame. For example GQ117034 also lacks it. So it is not just a sequencing error, or one clone lacking it. I do not know how important the PB1-F2 protein is, for viral “fitness” or pathogenicity or anything.

  • http://www.virology.ws profvrr

    The two mutations you mention could occur very easily. For a 10 kb
    viral RNA, there is one new mutation incorporated per new molecule
    synthesized. If 10,000 viral RNA molecules are made per cell (not
    unreasonable) then all genome positions could be altered. The point is
    that two base changes are no obstacle to an RNA virus. The question is
    whether making the F2 protein would be compatible with the replication
    of this particular virus, to which we don't yet have an answer.

  • John Rogans MD

    The big question seems to be –

    Can the current H1N1 virus mutate and somehow acquire the PB1-F2 protein and become a killer?

    JR, MD

  • http://www.virology.ws profvrr

    An interesting addition to the Nature paper would have been to mutate
    the 2009 H1N1 virus so that full-length PB1-F2 is produced, and then
    determine the virulence of the virus in animals. It's not clear to me
    that making PB1-F2 is all that would be needed to increase virulence
    of the H1N1 S-OIV virus in humans.

  • John Rogans MD

    One of the truly deadly features of the 1918 isolates was, I believe a replication rate of 40,000. (If that is the correct terminology. I am not a virologist.) Is there a comparable value for the 2009 virus?

    JR, MD

  • http://www.virology.ws profvrr

    I'm not sure what you are referring to. Perhaps the R value – the
    average number of secondary infections resulting from one infected
    host? The R value for the 1918 virus has been estimated at 2-3. I've
    seen similar numbers for the 2009 H1N1 virus.

  • http://www.virology.ws profvrr

    I'm not sure what you are referring to. Perhaps the R value – the
    average number of secondary infections resulting from one infected
    host? The R value for the 1918 virus has been estimated at 2-3. I've
    seen similar numbers for the 2009 H1N1 virus.

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