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Background  In Japan, a part of confirmed patients’ samples have been screened for the variant of concern (VOC), including the variant alpha with N501Y mutation. The present study aimed to estimate the actual number of cases with variant alpha and reconstruct the epidemiological dynamics.    Methods  The number of cases with variant alpha out of all PCR confirmed cases was estimated, employing a hypergeometric distribution. An exponential growth model was fitted to the growth data of variant alpha cases over fourteen weeks in Tokyo.    Results  The weekly incidence with variant alpha from 18–24 January 2021 was estimated at 4.2 (95% confidence interval (CI): 0.7, 44.0) cases. The expected incidence in early May ranged from 420–1120 cases per week, and the reproduction number of variant alpha was on the order of 1.5 even under the restriction of contact from January-March, 2021, Tokyo.    Conclusions  The variant alpha was predicted to swiftly dominate COVID-19 cases in Tokyo, and this has actually occurred by May 2021. Devising the proposed method, any country or location can interpret the virological sampling data.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12976-021-00146-x.

Estimating COVID-19 cases infected with the variant alpha (VOC 202012/01): an analysis of screening data in Tokyo, January-March 2021