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Commentary
Indiana H3N2v
Outbreak Raises Concerns
Recombinomics
Commentary 21:30
June 27, 2013
All individuals visited the Grant County Agricultural Fair, June 16-22, prior to illness,
The above comments from the Indiana State Health Department represent the third year in a row where the first H3N2v cases for the summer swine flu season were from Indiana (see map). However, the above cases are the earliest reported cases for the season.
In 2011 the first case was noted in late August based on sequences deposited by the CDC at GISAID, which were generated from a July 27 collection. The case (2M) was not directly linked to swine, but his caretaker had prior contact with swine at a fair. The sequence of the isolate, A/Indiana/08/2011, was the first human H3N2v case with an H1N1pdm09 M gene, That Indiana case was followed by confirmation of 3 cases at the Washington County fair in Pennsylvania, which at the time were the most H3N2v confirmed cases reported from the same venue. However, a follow-up study involving calls to 4-H members for participated in the fair identified 4 additional cases based on H3N2v antibody levels, as well as 81 additional cases with flu-like symptoms, which are uncommon in Pennsylvania in August. The three Pennsylvania sequences, as well as sequences from all subsequent H3M2v cases had an H1N1pdm09 M gene. The subsequent isolates from Indiana, Maine, and Iowa were closely related to the Indiana sequences.
However, at the end of 2011 an outbreak at a day care center in West Virginia involved H3N2v (A/West Virginia/06/2011) with an N2 from a different lineage (from H3N2v instead of H1N2v) and that constellation became dominant in human cases. The first 2012 case was in March in Utah, but the first case linked to fairs was again in Indiana. The La Porte fair outbreak was reported on July 26 with sequences from collections on July 16. The 2012 had many more case (309 vs 12 in 2011) and outbreaks were larger. The Gallia Fair outbreak in Ohio involved 100’s of attendees. The first 200 with symptoms were tested with an influenza A raid test and the 69 positives indicated virtually all were infected since the sensitivity of the rapid test was below 40%. Only 12 confirmed cases were reported by Ohio as well as 3 from West Virginia who also attended the fair, but the 200 attendees tested represented a subset of cases with symptoms.
The USDA monitors swine and prior to the explosion of cases in 2012, the H3N2 in swine matched the human cases from early 2011 (and N2 from H1N2v). However, all of the human cases matched the West Virginia sub-clade (N2 from H3N2v), with the exception of three cases from Michigan with a novel constellation.
Swine isolates from swine infected after the explosion of cases in 2012 are dominated by the human constellation. This week the USDA released sequences from seven 2013 isolates from Indiana. One had a H1N1pdm09 M gene with H3 and N2 lineages not found in human cases. However, the other six ((A/swine/Indiana/A01260252/2013, A/swine/Indiana/A01260254/2013, A/swine/Indiana/A01260261/2013, A/swine/Indiana/A01260276/2013, A/swine/Indiana/A01260280/2013, A/swine/Indiana/A01260284/2013) matched the human cases, raising concerns that the number of 2013 H3N2v cases will be significantly higher than the levels reported in 2012.
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