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 (n = 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) serving as a reference for selecting appropriate treatments, ii) enabling early detection of VOCs, iii) contributing to the development of hospital infection control guidelines, iv) fostering cooperation with local governments, v) supporting cohort studies, and vi) 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.

In the context of public health, asymptomatic carriers of respiratory infectious diseases are considered a hidden yet critical factor in the transmission of infection and represent a key target for efforts to mitigate disease spread. To contribute a unique genomic resource to the SARS-CoV-2 research community, we collected SARS-CoV-2–positive samples from asymptomatic individuals at the SB Coronavirus Inspection Center Corp. during the COVID-19 pandemic in Japan and conducted a comprehensive analysis of their viral genomes. Using Illumina COVIDSeq technology, we successfully generated 8,266 SARS-CoV-2 genome assemblies, all of which have been made publicly available to facilitate further research. In this report, we summarize our efforts to collect SARS-CoV-2–positive samples from asymptomatic individuals and highlight the key features and accessibility of this genomic dataset.

In the context of public health, asymptomatic carriers of respiratory infectious diseases are considered a hidden yet critical factor in the transmission of infection and represent a key target for efforts to mitigate disease spread. To contribute a unique genomic resource to the SARS-CoV-2 research community, we collected SARS-CoV-2–positive samples from asymptomatic individuals at the SB Coronavirus Inspection Center Corp. during the COVID-19 pandemic in Japan and conducted a comprehensive analysis of their viral genomes. Using Illumina COVIDSeq technology, we successfully generated 8,266 SARS-CoV-2 genome assemblies, all of which have been made publicly available to facilitate further research. In this report, we summarize our efforts to collect SARS-CoV-2–positive samples from asymptomatic individuals and highlight the key features and accessibility of this genomic dataset.

Saliva specimens are widely used for coronavirus disease 2019 (COVID-19) testing using RT-qPCR due to their advantages over nasopharyngeal swabs of being non-invasive and self-collectable. However, saliva collection can be time-consuming in individuals with reduced saliva secretion, including those with diabetes, diseases involving salivary glands such as Sjögren’s syndrome, and older adults. In this study, we evaluated the diagnostic performance of mouth rinse specimens, which can be easily collected even from individuals with reduced saliva secretion, as an alternative to saliva for RT-qPCR COVID-19 testing. Among the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive specimens analyzed, 88.2% were derived from patients possessing risk factors associated with reduced salivary secretion, including diabetes, use of medications such as anticholinergics or antihistamines, smoking, and older age. The analysis results of mouth rinse specimens demonstrated 96.7% overall agreement with those of saliva specimens, with a sensitivity of 94.1% and specificity of 100%; however, the viral load in the mouth rinse specimens was lower than that in saliva because of sample dilution. These findings suggest that mouth rinse specimens are a practical, versatile, and reliable alternative specimen for RT-qPCR COVID-19 testing.