Recombinomics Commentary 13:29
June 1, 2009
The latest surveillance report (week 20) from the CDC, clearly indicates that swine H1N1 activity is on the rise in the United States, as seasonal flu levels continue to decline. Consequently the ratio of swine H1N1 to seasonal flu (H1N1, H3N2, influenza B, combined) is greater than 10 to 1. Thus, the vast majority of influenza infections in the United States are now swine flu, which is clear from the latest figures, even though reporting agencies in the United States are limiting testing (see updated map). The latest figures show 1213 (1096+117) swine H1N1 cases compared to a total of 121 for seasonal flu (24+70+27). More importantly however, is the steady increase in the percentage of samples which are positive, (now at 22.41%), which is a frequent characteristic of seasonal flu at the height of flu season.
Although various government agencies had offered optimistic reassurances that the swine flu levels would decline during the summer “off season”, the latest data case serious doubt on that projection. The swine H1N1 has an avian PB2, which has an E at position 627. Consequently, the replication rate for the virus is optimal at 41 C, the body temperature of a bird. This is in marked contrast to seasonal flu, which had E627K, which optimizes replication rates to 33 C. Consequently, the swine H1N1 has increased activity as the weather warms in the northern hemisphere, and seasonal flu has declined as summer months approach.
This increase in H1N1 swine flu has been masked to varying degrees by reporting protocols. In Mexico, the national reports are limited to confirmed cases, and there is a large backlog in confirming probable cases. Thus, the reported numbers in Mexico grossly underestimates cases that have been lab confirmed (considered probable because they are influenza A positive, but not sub-typable with human flu reagents).
In the Unites States, the confirmatory tests have been shifted from the CDC to the 44 states that are certified to run the confirmatory tests. However, the number of confirmatory test kits is limited, so many states have focused on hospitalized patients and have stopped testing mild cases. Similarly, testing of school clusters is also limited to initial cases. The vast majority of infected students and teachers are also not tested. However, in spite of these limitations, the frequency of H1N1 swine positives has risen steadily.
These increases in the United States have begun to affected surveillance programs by countries outside of North America. An increasing number of cases link back to the United States. However, the programs in these other countries also grossly underestimates the number of cases, because the case definition includes travel from an H1N1 infected region, so local cases are not tested unless they link back to imported cases. However, this airport surveillance program misses the vast majority of imported cases because cases infected within a few days of travel are not symptomatic, and a high percentage of cases do not develop a high fever. Moreover, the rapid test used to confirm cases has a low sensitivity. Consequently, most imported cases are not detected, and local infected patients are also not tested because they do not meet the case definition.
This lack of testing is the used to claim that there has been no “evidence” of sustained community transmission, because the local cases are not tested until. However, this limited testing still identifies community cases which happen to be linked to a transmission chain under investigation. Similarly, the local cases lead to school outbreaks, which are not easily ignored, especially in countries in the northern hemisphere, because seasonal flu season has ended, so outbreaks involving students with flu-like symptoms leads to limited swine flu testing.
However, the large number of cases being reported daily, is leading to additional testing and additional examples of community transmission, which will clearly demonstrate that the pandemic is at phase 6. Redefining phase 6 to include severity of disease will just delay the inevitable, because the swine H1N1 will continue to adapt to its new host, which will likely lead to an increase in fatal cases, which involves the same age group (25-44), which was reported in for the initial cases in Mexico.