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Media Myths on trH3N2 Emergence and Significance
Recombinomics Commentary 21:20
November 25, 2011

Schaffner notes that flu viruses mutate and swap genes all the time. Infectious disease experts may only be noticing these new viruses because of better technology, he says. The USA's beefed-up state medical labs, which have lots more firepower than before 2001, are much better at spotting novel viruses, which in the past might have gone unnoticed.

Thanks to the sophistication of these labs, scientists are getting a window into the inner workings of the flu that they haven't had in the past, Schaffner says. But that doesn't mean that these novel viruses are necessarily any more dangerous.

The above comments are ironic, because it is the technology that paints a clear picture of the new human contagion, trH3N2, which is clearly ignored in the above comments.  The evolution is clearly demonstrated in the recent sequences, which show that in 2010 the trH3N2 was adapting to humans, leading to a clustering of human isolates in phylogenetic analysis.

The CDC release of the sequences from the prior human cases, coupled with enhanced surveillance of swine generated the genetic landscape of these viruses relative to swine sequences.  Prior to the 2009 pandemic, the triple reassortant H1 sequences were scattered and intermingled with swine sequences, but the clustering began in earnest a year ago, when WHO issued the pager alert.

Phylogenetic analysis was needed to see the relationship between the adapting sequences in 2010, and the emerging sequences in 2011, but the acquisition of the M gene from H1N1pdm provided the change that is easily cited and present in all human trH3N2 in 2011, but only in one swine isolate,

Many of the reports by the CDC have missed this point, including the most recent “Have Your Heard", which falsely claimed that this novel constellation was in swine in many states, when the number of reported cases remains at one, which was just reported earlier this month.  This narrative on swine exposure also distorts the testing needs, which is for samples that are not from patients with swine exposure, in contrast to the CDC’s request for samples in the MMWR on the first two cases, and the recent large Iowa cluster, which did not involved swine exposures.

The novel trH3N2 is dangerous and signals a second pandemic in three years, which is unprecedented but linked to the co-evolution of swine trH1N1 (H1N1pdm09) and swine H3N2 (H3N2pdm11) co-circulating in a human population.

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