The seasonal flu vaccine usually protects against three or four strains of the flu, which are chosen based on predictions for what will circulate in the US that year. According to the CDC, this year's flu shot included an influenza A H1N1, an influenza A H3N2, and an influenza B/Victoria lineage virus. So if H3N2 was included in the flu shot, why is it still making people sick?
H3N2 is, historically, a vicious strain of flu. So if it's the predominant strain, that season can still be severe even if people have some background exposure or immunity, Fauci says. H3N2 also mutates quickly, so the "reference strain" included in the flu shot may differ slightly from the H3N2 strain that shows up during flu season, lowering the vaccine's effectiveness.
“Even at its best, the seasonal flu vaccine is only 60% effective, and we’ve had years where it’s as low as 10% but we anticipate it won't be that low this year,” Fauci says. Experts won't know how effective the 2017–2018 flu vaccine is until the flu season is over, but the experts are predicting that it will be around 30% effective. This is much higher than Australia's flu vaccine, which was only 10% effective against H3N2.
That being said, the flu shot also protects against H1N1 and influenza B, which are circulating this year and tend to have a higher vaccine effectiveness than H3N2, Brammer says.