Monitoring reported SARS-CoV-2 variants to assess the status of COVID-19 epidemics in the low epidemic state

The reported new confirmed cases of Coronavirus Disease 2019 (COVID-19) nowadays have diminished in their usefulness for assessing the pandemic situation. This study aimed to discover the correlation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants recorded by Nextstrain clade and PANGO lineage and the number of new confirmed cases. Percent stacked area charts were utilized to display their development trends. 31 and 1452 variants were named according to Nextstrain clade and PANGO lineage, respectively. The branch step value maintained a stable increase by linear regression analysis. The changing trend in SARS-CoV-2 variants (PANGO lineage) correlated negatively with the number of new confirmed COVID-19 cases through Spearman rank correlation coefficient (17/06/2020-17/11/2021, ρ=-0.387, P < 0.01; 15/12/2021-11/01/2023, ρ=-0.458, P < 0.01). The proportion and composition of dominant virus variants had regional discrepancies, but some also fluctuated. The speed and quantity of SARS-CoV-2 variants objectively reflect the characteristics of the COVID-19 pandemic and viral dissemination in the population even without valuable data of reported new confirmed cases. The SARS-CoV-2 variation may be a better tool for epidemic monitoring and early-warning in the low epidemic state.