Early Warning Surveillance for SARS-CoV-2 Omicron Variants, United Kingdom, November 2021-September 2022

Abstract

Since June 2020, the SARS-CoV-2 Immunity and Reinfection Evaluation (SIREN) study has conducted routine PCR testing in UK healthcare workers and sequenced PCR-positive samples. SIREN detected increases in infections and reinfections and delected Omicron subvariant waves emergence contemporaneous with national surveillance. SIREN's sentinel surveillance methods can be used for variant surveillance.

Keywords: BA.1; BA.2; BA.4; BA.5; COVID-19; Omicron variant; SARS; SARS-CoV-2; SIREN study; United Kingdom; coronavirus; coronavirus disease; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.

Figure 1

Rate of SARS-CoV-2 infections and reinfections detected through SIREN early warning system, United Kingdom, June 2020–September 2022. The SIREN study tested healthcare workers every 2 weeks via PCR and sequenced PCR-positive samples. We considered primary infection as infections among participants without prior infection and reinfections as infections among persons with prior infection. SIREN, SARS-CoV-2 Immunity and Reinfection.

Figure 2

Number of sequenced samples by variant per week in SIREN early warning system, United Kingdom, March 2020–June 2022. The SIREN study tested healthcare workers every 2 weeks via PCR and sequenced PCR-positive samples. We have plotted all samples successfully sequenced and assigned a variant call or unclassified lineage. Dates of detection are noted for each variant. Of note, among >44,000 UK healthcare workers from 135 secondary care health organizations, we detected 521 cases of unclassified variants, 323 cases of Alpha, 1,042 cases of Delta, 83 cases of Delta plus, 1,487 cases of Omicron BA.1, 1,514 cases of Omicron BA.2, 4 cases of XE, 51 cases of Omicron BA.4, and 236 cases of Omicron BA.5. SIREN, SARS-CoV-2 Immunity and Reinfection.