Decrease in RT-PCR Ct values among SARS-CoV-2 positive samples during the emergence of the B.1.617.2 (Delta) variant in Malaysia

Abstract

The RT-PCR cycle threshold (Ct) value for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is inversely proportionate to the virus load in the patient’s specimen. These values could be beneficial to be used in monitoring the epidemic trajectory at the population level. The SARS-CoV-2 B.1.617.2 (Delta) variant which emerged in late 2020, caused an unprecedented exponential increase in SARS-CoV-2 infection cases worldwide. In Malaysia, the surge in coronavirus disease 2019 (COVID-19) cases and the inclining positivity rate contributed to the epidemic waves started in late May 2021. The sudden surge in cases was speculated to be associated with increased transmission caused by the emergence of the B.1.617.2 variant. This could be reflected by changes in the mean Ct value distribution which reflects the viral load in the population. In the present study, the Ct value distribution of COVID-19 infected person samples from the years 2020 and 2021 were tabulated against the SARS-CoV-2 genomic variants determined from genomic sequencing. A significant decreasing pattern of the mean Ct values from the overall 2020 and 2021 samples were noted (p<0.01). There was, however, high variability in the Ct values of samples obtained between 2020 and 2021 in contrast to samples with lower mean Ct value obtained in 2021. The percentages representation of SARS-CoV-2 genomic variants B.1.36 and B.1.524 were 31.6% and 68.4%, respectively, for samples obtained in October and December 2020. Whereas samples obtained in June and July 2021 were 100% of the B.1.617.2 variant. The decreasing trend in the Ct value distribution from samples tested in our laboratory correlated well with the increasing weekly COVID-19 cases reported by the Malaysia national data which was subsequently attributed by the emergence of B.1.617.2 in the country. This study suggests that the Ct value distribution of samples taken from the screening of SARS-CoV-2 infected population could provide insight into the potential epidemiologic transmission dynamic at the population level and when coupled to the virus genomic sequencing surveillance could allow detection of an emerging SARS-CoV-2 variant with different transmission behaviour. This could facilitate early response control strategies to limit the transmission of an emerging SARS-CoV-2 variant.