The astrophysical $S$-factor for the radiative capture $d(p,gamma)^3$He in the energy-range of interest for Big Bang Nucleosynthesis (BBN) is calculated using an {it ab-initio} approach. The nuclear Hamiltonian retains both two- and three-nucleon interactions - the Argonne $v_{18}$ and the Urbana IX, respectively. Both one- and many-body contributions to the nuclear current operator are included. The former retain for the first time, besides the $1/m$ leading order contribution ($m$ is the nucleon mass), also the next-to-leading order term, proportional to $1/m^3$. The many-body currents are constructed in order to satisfy the current conservation relation with the adopted Hamiltonian model. The hyperspherical harmonics technique is applied to solve the $A=3$ bound and scattering states. A particular attention is used in this second case in order to obtain, in the energy range of BBN, an uncertainty on the astrophysical $S$-factor of the order or below $sim$1 %. Then, in this energy range, the $S$-factor is found to be $sim$10 % larger than the currently adopted values.Part of this increase (1-3 %) is due to the $1/m^3$ one-body operator, while the remaining is due to the new more accurate scattering wave functions. We have studied the implication of this new determination for the $d(p,gamma)^3$He $S$-factor on deuterium primordial abundance. We find that the predicted theoretical value for $^2$H/H is in excellent agreement with its experimental determination, using the most recent determination of baryon density of Planck experiment, and with a standard number of relativistic degrees of freedom $N_{rm eff}=3.046$ during primordial nucleosynthesis.
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