Large-scale screening of SARS-CoV-2 variants in Tokyo, Japan: A 3-year and 9-month longitudinal survey

Over nearly four years (March 10, 2021-December 31, 2024), we performed a comprehensive longitudinal analysis of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants among patients in a single hospital in Tokyo, Japan. Using RT-qPCR and Sanger sequencing, complemented by whole-genome sequencing, we tested nasopharyngeal swab samples (<i>n</i> = 4,628) and tracked the emergence and evolution of variants of concern (VOCs). The findings demonstrate the utility of a hospital-based SARS-CoV-2 variant surveillance system for informing clinical decision-making and public health settings, including: <i>i</i>) serving as a reference for selecting appropriate treatments, <i>ii</i>) enabling early detection of VOCs, <i>iii</i>) contributing to the development of hospital infection control guidelines, <i>iv</i>) fostering cooperation with local governments, <i>v</i>) supporting cohort studies, and <i>vi</i>) identifying long-term SARS-CoV-2 infections. This work underscores the importance of real-time variant monitoring for mitigating the effects of pandemics and provides essential epidemiological and clinical data that can guide future outbreak management and policy development.