Recombinomics: Swine H1N1 Outpaces Seasonal Flu In the United States

Recombinomics Commentary 21:51
May 12, 2009
The week 17 CDC report on seasonal flu in the United States was striking. The normal bell shaped curve of cases detected by CDC sentinel labs was suddenly interrupted by a sharp spike. Although the height of the spike was driven somewhat by increased surveillance due to the detection of H1N1 swine, the composition of the bar representing week 17 was a clear signal that swine H1N1 had taken change of influenza cases in the US. The initial data for influenza had 334 and 300 positives for H1 and H3, respectively, but there were 326 and 304 isolates for swine H1N1 or untypable influenza A (which is swine H1N1 that has not yet been confirmed). The updated data posted this week was even more striking, with 370 and 342 isolates for H1 and H3 respectively, while swine H1N1 and untypable influenza A were 524 and 259. Thus, there was more swine H1N1 than the combination of H1 and H3 seasonal flu.

The spike in H1N1 swine cases created a backlog at the CDC, which could be seen in a map of confirmed and probable cases (see US map). The confirmatory testing was handed off to the state labs to eliminate the backlog, but soon state labs were acknowledging that the samples tested were the tip a very large iceberg, and future testing would target more serious cases.

This movement of swine H1N1 into the human population is cause for concern. The increase over seasonal flu may be driven by the avian PB2 gene in the swine isolate. Position 627 is E, which favors growth at the higher body temperature of birds. Seasonal flu has a K at position 627, which allows for more rapid replication at a lower temperature, which is consistent with the internal temperature of a human nose in the winter.

The presence of avian PB2 may offer a selective advantage over the summer, when seasonal flu falls to barely detectable levels. However, the swine H1N1 that moves south in the upcoming months will be growing under colder conditions, which may favor the acquisition of E627K though reassortment or recombination. This change could create a more virulent H1N1 in the fall in the northern hemisphere.

Thus, the swine H1N1 may be launching a two virus strategy. The H1N1 with avian PB2 will dominate in the northern hemisphere over the summer, while the H1N1 in the southern hemisphere will acquire E627K and establish dominance during the winter months.

Thus, the spread of H1N1 is in high gear, as WHO debates if a swine H1N1 is a swine H1N1 and if a pandemic at phase 6 is really at phase 6.

Swine H1N1 doesn't read WHO press releases.

It just gains transmission efficiencies via homologous recombination.

Media Link