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In the standard theory of superconductivity, the origin of superconductivity is the electron-pairing. The induced current by a magnetic field is calculated by the linear response to the vector potential, and the supercurrent is identified as the dissipationless flow of the paired-electrons, while single electrons flow with dissipation. This supercurrent description suffers from the following serious problems: 1) it contradicts the reversible superconducting-normal phase transition in a magnetic field observed in type I superconductors; 2) the gauge invariance of the supercurrent induced by a magnetic field requires the breakdown of the global $U(1)$ gauge invariance, or the non-conservation of the particle number; 3) the explanation of the ac Josephson effect is based on the boundary condition that is different from the real experimental one. We will show that above problems are resolved if the supercurrent is attributed to the collective mode arising from the Berry connection for many-body wave functions. The problem 1) is resolved by attributing the appearance and disappearance of the supercurrent to the abrupt appearance and disappearance of topologically-protected loop currents produced by the Berry connection; the problem 2) is resolved by assigning the non-conserved number to that for the particle number participating in the collective mode produced by the Berry connection; and the problem 3) is resolved by identifying the relevant phase in the Josephson effect is that arising from the Berry connection, and using the modified Bogoliubov transformation that conserves the particle number.