In the development of an inactivated virus vaccine, the isolation of a single virus strain plays a key role in determining potency. The conventional methods of quantification of virus number are mainly based on virus titers, which are subjective and time-consuming, especially in the early stage of virus isolation, in which the titer difference is weak. Previous reports have shown a high correlation between the spike protein and the potency of COVID-19 vaccines. In this paper, we report a novel, fast, and convenient method of screening an Omicron virus strain by quantifying the spike protein content, where the isolated strain shows high affinity to Omicron-specific antibodies and a high titer, and it can induce high levels of neutralization antibodies.