In Japan, a prioritized COVID-19 vaccination program using Pfizer/BioNTech messenger RNA (mRNA) vaccine among healthcare workers commenced on February 17, 2021. As vaccination coverage increases, clusters in healthcare and elderly care facilities including hospitals and nursing homes are expected to be reduced. The present study aimed to explicitly estimate the protective effect of vaccination in reducing cluster incidence in those facilities. A mathematical model was formulated using three pieces of information: (1) the incidence of clusters in facilities from October 26, 2020 to June 27, 2021; (2) the incidence of confirmed COVID-19 cases during the same period; and (3) vaccine doses among healthcare workers from February 17 to June 27, 2021, extracted from the national Vaccination System database. We found that the estimated proportion at risk in healthcare and elderly care facilities declined substantially as the vaccination coverage among healthcare workers increased; the greater risk reduction was observed in healthcare facilities, at 0.10 (95% confidence interval (CI): 0.04-0.16) times that in the pre-vaccination period, while that in elderly care facilities was 0.34 (95% CI: 0.24-0.43) times that in the earlier period. The averted numbers of clusters in healthcare facilities and elderly care facilities were estimated to be 247 (95% CI: 210-301) and 279 (95% CI: 218-354), respectively. Prioritized vaccination among healthcare workers had a marked impact on preventing the incidence of clusters in facilities.
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