High proportion of low cycle threshold value as an early indicator of COVID-19 surge.

Many countries in the world are experiencing a recent surge in COVID-19 cases. This is mainly attributed to the emergence of new SARS-CoV-2 variants. Genome sequencing is the only means to detect the evolving virus mutants and emerging variants. Cycle threshold values have an inverse relationship with viral load and lower Ct values are also found to be associated with increased infectivity. In this study, we propose to use Ct values as an early indicator for upcoming COVID-19 waves. A retrospective cross-sectional study was carried out to analyze the Ct values of positive samples reported during the first wave and second wave (April 2020-May 2021). Median Ct values of confirmatory genes were taken into consideration for comparison. Ct values below 25, >25-30, and >30 were categorized as high, moderate, and low viral load respectively. Our study found a significantly higher proportion of positive samples with a low Ct value (<25) across age groups and gender during the second wave of the COVID-19 pandemic. A higher proportion of positive samples with a low Ct value (high viral load) may act as an early indicator of an upcoming surge.