We calculate the quadratic fluctuations of net baryon number, electric charge and strangeness as well as correlations among these conserved charges in (2+1)-flavor lattice QCD at zero chemical potential. Results are obtained using calculations with tree level improved gauge and the highly improved staggered quark (HISQ) actions with almost physical light and strange quark masses at three different values of the lattice cut-off. Our choice of parameters corresponds to a value of 160 MeV for the lightest pseudo scalar Goldstone mass and a physical value of the kaon mass. The three diagonal charge susceptibilities and the correlations among conserved charges have been extrapolated to the continuum limit in the temperature interval 150 MeV <T < 250 MeV. We compare our results with the hadron resonance gas (HRG) model calculations and find agreement with HRG model results only for temperatures T<= 150 MeV. We observe significant deviations in the temperature range 160 MeV < T < 170 MeV and qualitative differences in the behavior of the three conserved charge sectors. At T < 160 MeV quadratic net baryon number fluctuations in QCD agree with HRG model calculations while, the net electric charge fluctuations in QCD are about 10% smaller and net strangeness fluctuations are about 20% larger. These findings are relevant to the discussion of freeze-out conditions in relativistic heavy ion collisions.