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Vaccine developers and WHO suggest individuals to receive multiple vaccinations (the primary and the secondary vaccinations and booster shots) to mitigate transmission of COVID-19. Taking this into account, we include compartments for multiple vaccinations and mutant viruses of COVID-19 in the model. In particular, our model considers breakthrough infection according to the antibody formation rate following multiple vaccinations. We obtain the effective reproduction numbers of the original virus, the Delta, and the Omicron variants by fitting this model to data in Korea. Additionally, we provide various simulations adjusting the daily vaccination rate and the timing of vaccination to investigate the effects of these two vaccine-related measures on the number of infected individuals. We also show that starting vaccinations early is the key to reduce the number of infected individuals. Delaying the start date requires increasing substantially the rate of vaccination to achieve similar target results. In the sensitivity analysis on the vaccination rate of Korean data, it is shown that a 10% increase (decrease) in vaccination rates can reduce (increase) the number of confirmed cases by 35.22% (82.82%), respectively.<\/jats:p>","DOI":"10.1371\/journal.pone.0275851","type":"journal-article","created":{"date-parts":[[2022,10,24]],"date-time":"2022-10-24T17:26:18Z","timestamp":1666632378000},"page":"e0275851","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":13,"title":["A model of COVID-19 pandemic with vaccines and mutant viruses"],"prefix":"10.1371","volume":"17","author":[{"given":"Young Rock","family":"Kim","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong-Jae","family":"Choi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5338-1722","authenticated-orcid":true,"given":"Youngho","family":"Min","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,10,24]]},"reference":[{"issue":"4","key":"pone.0275851.ref001","doi-asserted-by":"crossref","first-page":"2000058","DOI":"10.2807\/1560-7917.ES.2020.25.4.2000058","article-title":"Pattern of early human-to-human transmission of Wuhan 2019 novel coronavirus (2019-nCoV), December 2019 to January 2020","volume":"25","author":"J. 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