Odd mutation pattern in flu

The seasonal flu's newfound and widespread drug resistance was made possible by an odd series of mutations -- at least two "permissive" mutations that evolved before the mutation for resistance even occurred, according to a study published this week in Science.

A graphical depiction of the neuraminidase (NA) molecule
with the resistance mutation (H274Y) shown in pink.
The two compensatory mutations (V234M and R222Q)
at the sites shown in orange may help the protein
folding in a way that rescues viral fitness in the
presence of the H274Y mutation.
(The figure was generated using the atomic coordinates
from a crystal structure (PDB ID. 3CL0) on Pymol.)
Image: Kalyan Das (kalyan@cabm.rutgers.edu)
CABM & Rutgers University, NJ

The results point to a possible method for predicting which strains of flu are more likely to evolve such resistance in the future. "This is a neat story," said structural biologist linkurl:Kalyan Das;https://www.cabm.rutgers.edu/%7Ekalyan/ of the Center for Advanced biotechnology and Medicine at Rutgers University, who was not involved in the research. "Usually, the understanding [is] first resistance mutations occur, and then the virus is less fit, [and] then the compensatory mutations occur to make the viruses more fit. But [here], the secondary mutations set the foundation for the resistance mutation." Influenza A wreaks havoc on populations around the world each winter, particularly in the past few years, when the seasonal virus seems to have evolved widespread resistance to the world's primary line of defense against it -- the antiviral drug oseltamivir (or Tamiflu). The virus's resistance to this drug is a result of a single amino acid substitution, known as H274Y, in a protein called neuraminidase. While the H274Y mutation has been around for nearly 10 years, until recently, it was very rare, due to the fact that in addition to offering drug resistance, it also impaired viral growth. But something clearly changed prior to the 2007-2008 flu season, when reports of oseltamivir resistance started popping up around the world. One possible explanation for such a rapid increase in resistant viral strains is the occurrence of secondary mutations, which somehow compensate for the decrease in viral fitness associated with H274Y. Examining mutations that occurred in flu strains in the years leading up to the 2007-2008 flu season, biologist linkurl:Jesse Bloom;https://baltimorelab.caltech.edu/personnel.html and his colleagues at the California Institute of Technology identified two such mutations at distant sites in the neuraminidase molecule. H274Y viruses lacking these additional mutations showed significantly less growth than wild-type viruses; viruses with all three mutations, however, were as hardy as wild-type ones. Furthermore, the triple mutants grew just as well when the researchers added oseltamivir to the cell cultures as they did in the absence of the drug, while the wild-type viruses hardly grew at all. Interestingly, the researchers found, in the lineages containing all three mutations, the two compensatory mutations actually occurred prior to the H274Y mutation, suggesting that they were "permissive," allowing the H274Y to spread through the population rather than be lost as a result of its deleterious effects on viral fitness. "Typically it's very hard to figure out whether the secondary mutation was permissive in the sense that it occurred before or it was compensatory in the sense that it occurred after the [resistance] mutation," Bloom said, but thanks to the extensive genotype data available for flu strains from the last 10 years, "we've been able to resolve [this question]." Although not commonly documented, "this kind of phenomenon may be rather widespread," Bloom added. If true, identifying such permissive mutations could allow researchers to predict which flu strains may be more likely to evolve drug resistance. It "is quite compelling [as] a way to look in advance [at] the development of drug resistance viruses," said immunologist and virologist linkurl:Wayne Marasco;https://physicians.dana-farber.org/directory/profile.asp?dbase=main&setsize=10&display=Y&nxtfmt=pc&gs=adf&picture_id=0000265&lookup=Y&pict_id=0000265 of the Dana-Farber Cancer Institute at Harvard Medical School. However, he added, such resistance may be permitted by more than just the two mutations identified in this study. "In order to do this at the global scale, you have to ask if other mutations in the virus [can] lead to [the] neutralizing of a negative mutation." When we start to look at different viruses, Bloom agreed, there may be a "range of permissive mutations available to the viruses." A lingering question is how these mutations arose in the first place. One possibility is that the mutations may have "hitchhiked" their way into the viral genome, fortuitously linked to a beneficial mutation in some nearby gene. Alternatively, the two permissive mutations may provide some benefit to the virus even in the absence of H274Y. "One of the difficulties of looking at evolutionary questions is it's always very hard to prove why something happened in nature," Bloom said. Despite the somewhat fuzzy evolutionary history of the mutations, their identification and recognition that they occurred prior to the resistance mutation are big steps for the field, said Marasco. "It's potentially a high impact paper in terms of approaches to drug resistance." J.D. Bloom, et al., "Permissive secondary mutations enable the evolution of influenza oseltamivir resistance," Science, 328:1272-5, 2010.
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[23rd February 2009]