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H1N1 Swine Flu Levels Approach 100% In Texas and US
Recombinomics Commentary 04:00
December 23, 2013

Out of 10,472 laboratory-tested specimens in Texas during the 2013-14 flu season, 1,495 tested positive for influenza, with 417 testing positive for H1N1, according to the Texas Department of State Health Services’ Influenza Surveillance Information.

“According to our infectious disease specialists here at Memorial Hermann-Texas Medical Center, we’ve seen about 20 cases of influenza so far this month, some of which have been H1N1,” said Kathryn Klein, manager of external communications.

The above comments suggest that H1N1 levels in Texas are somewhere between one third and half of flu cases, when in fact the levels in Texas and the United States are approaching 100%.  The above impression is due to the widespread use of rapid tests, which significantly under-represents H1N1 cases.  On Friday Texas issued an influenza alert, warning physicians not to rely on rapid tests or delay treatment while waiting for retest data.  This warning was based in part by reports of a “mystery illness”. Conroe Regional Medical Center noted that 8 patients (including 4 who had died), who had textbook H1N1 (swine flu) symptoms, tested negative on a rapid test, while a PCR re-test on 3 or 4 of the survivors identified H1N1 in 1 or 2 of these cases (2 confirmed H1N1 cases were reported, but it is unclear if the second positive was from the 4 surviving cases re-tested).

Texas (along with 3 other southern states – Louisiana, Mississippi, and Alabama) has the highest ILI (influenza-like illness) in the United States (10 on a scale of 10).  The most recent weekly report (week 50) indicates almost all influenza A in Texas is H1N1, which is also true for the entire country.  The actual data significantly under-represents H1N1 because of widespread reliance of the rapid test, which has a notoriously low sensitivity for H1N1 (many fatal cases in 2009 were H1N1 confirmed at autopsy because multiple earlier rapid tests were falsely negative).

However, even without adjustments for the gross under-representation due to false negatives in the rapid tests, week 50 for Texas shows that 634/641 (98.9%) of samples that are influenza positive are positive for influenza A and 172/179 (96.0%) of the influenza A is H1N1.  Thus, 95.0% of influenza in Texas is H1N1, even without correction for the many H1N1 cases that are not considered because the false test negative on the rapid test.

Similar frequencies are seen nationwide in the CDC’s week 50 FluView. 1261/1301 (96.9%) on influenza positive samples are influenza A and 559/575 (97.2%) influenza A cases are H1N1.  Thus, nationwide 94.1% of flu cases are H1N1, even without adjustment for false negatives due to widespread use of the rapid test , which generate far more false negatives than true positives nationwide.

Thus, unadjusted numbers have H1N1 at 95.0% of all flu in Texas and 94.1% nationwide, but the actual frequency is close to 100% in Texas and throughout the country.

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