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CDC Ignores NA Lineage Change in All 2012 H3N2v Cases
Recombinomics Commentary 21:15
August 13, 2012

Helen Branswell: Thank you very much for taking my questions. Two quick questions. The first is, when you're looking at the viruses in the lab, do they all look identical? Are they all this virus with the m gene from the pandemic virus from 2009, and the second is, is there any consideration being given to asking fairs to not hold swine competitions this year in light of what's going on?

Joe Bresee: Thanks, Helen. I'll absolutely let you ask two questions. Thanks for the questions. The first question is easy. Yeah, these viruses are all the same. They're not completely genetically identical, but very close to being so. All the viruses we've seen so far in the increase in cases are the H3N2v viruses with the m gene as you say.

The above question and answer on the genetic composition of the H3N2v in the recent explosion of cases highlight the limitations in the teleconference which is driven by strongly held misconceptions.  The two questions assume that the M gene is the key driver for the 2012 cases and that these cases are due to H3N2v jumping from swine to human.

However, the sequence data (which were made public prior to the above August 9 teleconference), shows that the key driver in the 2012 cases is the NA gene, which was from a different lineage in the West Virginia cluster, which included 23 ILI cases, and the NA gene in the West Virginia cluster has been found in all eight 2012 cases, which are from 4 different states, and 7 of the 8 cases are from July infections.  Although this new constellation, which shares 7 of the 8 gene segments (including the M gene) with the initial 2011 cases but has an NA gene that was circulating in H3N2 swine isolates, in contrast to the 2011 human cases which had an NA gene circulating in H1N2 swine.  These two NA lineages are easily distinguished and the matches of the 2012 human cases with the West Virginia are unambiguous, which is also true for the differences between the two lineages.

However, although these differences are clear and have been noted since the sequences were released in 2011, the CDC has not addressed the change in the West Virginia cluster, or the appearance of the new constellation in all human cases.

Moreover, the CDC has not addressed the fact that this constellation is rare in swine isolates collected prior to the July outbreaks.

Thus, the reporters at the teleconference lack the basic understanding of the July 2012 sequences, which were made public prior to the above teleconference.

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