Use of TEM-PCR during H1N1 pandemic

Background: The emergence of novel swine-origin influenza A (H1N1) virus (S-OIV) infection represents a significant pandemic threat. Rapid and accurate diagnosis will enhance treatment and containment efforts

Objective: Evaluating the use of Target Enriched Multiplex Polymerase Chain Reaction (Tem-PCR) during intial 2009 H1N1 pandemic.

Methods: Ninety eight patients with influenza-like illness meeting the CDC’s guidelines for screening were tested with the rapid influenza test. Positive samples for influenza A were tested with real-time PCR (RT-PCR). Subsequently, all samples were tested using Target Enriched Multiplex Polymerase Chain Reaction (Tem-PCR) which can  detects targets specific for several upper respiratory viral pathogens, including differentiation of Influenza A, Influenza B and S-OIV.

Results: Rapid influenza antigen tests revealed 30 positive specimen for influenza A, 1 for influenza B, and 67 were negative. The 30 samples that were positive for influenza A were tested by the DOH and CDC with RT-PCR assay which revealed 2 cases of seasonal influenza A, 7 confirmed cases of S-OIV, and the remaining 21 samples were negative for influenza infection. The Tem-PCR confirmed 1 case of the seasonal influenza A cases but found the second case to be S-OIV. Tem-PCR confirmed the findings of RT-PCR in 3 of the S-OIV cases but found that 4 of the cases were negative for influenza. Additionally, Tem-PCR found 3 of the cases that were negative based on RT-PCR were positive for S-OIV. The remainders were confirmed negative for influenza but one was positive for adenovirus. The lone case of influenza B was confirmed with Tem-PCR. The 67 cases that were negative based on rapid influenza antigen test results were tested using Tem-PCR. Tem-PCR found that one case was positive for S-OIV but the rest of the cases were negative for influenza. Tem-PCR found several other organisms that the other tests could not detect. It found 1 case of adenovirus, 3 cases of coxsackievirus, 1 case of metapneumovirus, 4 cases of parainfluenzavirus, and 13 cases of rhinovirus. When comparing the rapid influenza tests to Tem-PCR in our study, we found the rapid tests to have a sensitivity and specificity of 90% and 76%, respectively, with a positive predictive value of 30% and a negative predictive value of 99%.

Conclusions: A well-validated rapid, sensitive, and specific test for confirming S-OIV is urgently needed. Beyond serving as a confirmatory test for S-OIV, Tem-PCR can detect other viral infections which may aid in reducing further measures recommended in cases of swine flu including treatment of contacts, isolation of patients leading to the loss of workdays, unnecessary treatment of patients, and possible lessening or avoidance of developing resistance to available antiviral pharmacotherapy. The identification of other viruses showed the clinical criteria for diagnosing this emerging infection are helpful but not specific for swine flu infection