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

N Che-Kamaruddin1, B T Teoh1, K K Tan1

  • 1Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia.

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Analyzing cycle threshold (Ct) values from RT-PCR tests can reveal SARS-CoV-2 transmission dynamics. Lower Ct values in 2021 correlated with the emergence of the Delta variant (B.1.617.2) and increased COVID-19 cases in Malaysia.

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Area of Science:

  • Virology
  • Epidemiology
  • Molecular Diagnostics

Background:

  • Reverse transcription-polymerase chain reaction (RT-PCR) cycle threshold (Ct) values are inversely proportional to viral load.
  • The emergence of SARS-CoV-2 variants, particularly B.1.617.2 (Delta), significantly impacted global infection rates.
  • Malaysia experienced substantial COVID-19 surges in 2021, coinciding with the Delta variant's prevalence.

Purpose of the Study:

  • To analyze the distribution of Ct values in relation to SARS-CoV-2 genomic variants in Malaysia.
  • To investigate the correlation between Ct values, viral variants, and COVID-19 epidemic trends.
  • To assess the utility of Ct value analysis for monitoring population-level transmission dynamics.

Main Methods:

  • Tabulation of Ct value distribution for positive COVID-19 samples from 2020 and 2021.
  • Genomic sequencing to identify SARS-CoV-2 variants (B.1.36, B.1.524, B.1.617.2).
  • Statistical analysis of Ct value trends and comparison with national COVID-19 case data.

Main Results:

  • A significant decrease in median Ct values was observed from 2020 to 2021 (p<0.01).
  • Samples from 2021 predominantly comprised the B.1.617.2 variant, exhibiting lower median Ct values compared to 2020 variants.
  • Decreasing Ct value trends correlated with increasing weekly COVID-19 cases in Malaysia.

Conclusions:

  • Ct value distribution analysis can effectively indicate population-level SARS-CoV-2 transmission dynamics.
  • The study highlights the association between the B.1.617.2 variant, lower Ct values, and increased COVID-19 cases.
  • Integrating Ct value analysis with genomic sequencing aids in early detection and control of emerging SARS-CoV-2 strains.