| Summary: | Early detection of increases in infections and/or new variants of SARS-CoV-2, is critical for public health response. In late 2020 we investigated if cycle threshold (Ct) data from PCR tests for SARS-CoV-2 could be analyzed to provide an early indicator of epidemic growth. We analyzed daily means of Ct values by gene-target and used iterative sequential regression to detect breakpoints in mean Ct values (and positive tests). We continued these analyses in realtime to monitor the epidemic in England. From Sept 2020 to Jan 2022, 7,611,153 PCR positive SARS-CoV-2 tests with Ct data were reported. Gene target (S+/S-) specific mean Ct values decreased 6-29 days prior to increases in positive test counts, and S-gene Ct values provided early indication of increasing new variants (Delta and Omicron). This approach had substantial benefit in the context of the first waves of the COVID-19 pandemic and can support future
infectious disease monitoring.
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