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Commentary
Maine trH3N2
Sequence Matches Signal Human Transmission
Recombinomics Commentary 16:00
November 19, 2011
• On October 30, 2011, partial genome sequencing confirmed the virus as a swine-origin triple reassortant influenza A (H3N2) virus with the M gene from pH1N1.
The above comments demonstrate the importance of sequencing in the confirmation of the trH3N2. The above case from Maine (8M, A/Maine/07/2011) was tested by the state lab using the newly approved CDC PCR influenza test, which includes the internal gene target, pdmNP. Although the primers are based on the sequence from H1N1pdm09, the NP gene is well conserved leading to cross reactivity between the H1N1pdm09 and trH3N2 NP genes.
The first case from Maine (8M, A/Maine/06/2011) was tested with the new kit, and was positive for the seasonal H3 test and the pdmNP, signaling a likely trH3N2 case, which was also confirmed by CDC sequencing. The sample from second case however, had a low level of RNA, leading to the seasonal H3N2 profile described above. However, since the second case attended the same agricultural fair (Fryeburg, ME) as the confirmed case, and also participated in one of the pig scrambles at the fair, and also was exposed to swine after the fair, the sample was forwarded to the CDC, where trH3N2 was rapidly confirmed by direct sequencing of the sample.
The low abundant RNA led to sequences represent short stretches (ranging from 230-319 BP) of four gene segments (HA, NP, MP, NS) which conclusively demonstrated that the trH3N2 was the same novel sub-clade that had been detected in six other trH3N2 cases from 2011. Moreover, the sequences had unique polymorphisms that were only present in the earlier trH3N2 case from Maine, indicating this regional sub-clade was circulating in Maine.
The two Maine case developed symptoms more than three weeks apart (Oct 7 and Oct 22), precluding transmission between the two cases, even though both attended the same fair. The end of the fair on Oct 9 also precluded it as a source of the infection of the second case, and testing by the Maine Department of Agriculture also failed to indentify SOIV in the symptomatic swine at the fair, reducing the likelihood that swine at the fair were the source of the trH3N2 infection in the first case. Similarly, the swine linked to the second case in the week prior to symptoms were asymptomatic, also reducing the likelihood that those swine were the source of the second case.
However, the virtual identity between sequences from the two case indicated the trH3N2 was widespread in Maine, leading to two confirmed cases in a two week period. The significance of these two positives was highlighted in the Maine weekly flu reports, which have only reported two positive flu cases this season, and the two cases were the two boys described above.
Neither of the two cases in Maine was hospitalized, and mild cases such as the two who had swine exposure are rarely sent to the Maine CDC for testing. This was documented in the video of one of the swine scrambles at the Fryeburg fair. The audio of the 6 minute 41 second upload clearly captured the coughing of a child who was either filming the scramble or standing next to the videographer. Thus, the symptomatic fair visitor raises concerns that the trH3n2 is widespread in Maine, but the limited testing has failed to capture those who were trH3N2 infected, but without swine exposure. The Maine CDC has requested samples from residents, but the trH3N2 advisory, which claimed that all prior 2011 trH3N2 had swine exposure, and comments by the Maine CDC’s epidemiologist, claiming no thought was given to human transmission of trH3N2 appears to have limited the number of influenza A positive sinces, since the only positives to date were the two trH3N2 cases.
An announcement that the symptomatic swine at the fair tested negative for SOIV, and the fact that the other swine associated with these cases were asymptomatic and an unlikely source of the trH3N2 would lead to an increase in influenza A samples from Maine residents.
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