now highly vaccinated (95%). The incidence of new infections and potential reinfections in SIREN is monitored and would be expected to rise if a new variant became highly prevalent and was able to escape predominantly vaccine-derived immunity. The frequency of PCR positivity in the SIREN cohort overall has increased in June, after very low levels March-May, but remains low (Figure 10). Of the 35 participants with a new PCR positive since April 2021 in the SIREN cohort overall, 28 (80%) occurred 14 days or more following their second vaccine dose. Reinfections remain at very low numbers in individuals previously either PCR positive or seropositive (Figure 11). *Number excludes participants who have withdrawn from the study and requested their data to be removed and participants recruited in hospitals in the devolved administrations. SARS-CoV-2 variants of concern and variants under investigation 32 Figure 10. PCR positivity within the SIREN study for all regions, England (fortnightly testing interval) Data up to 20 June 2021. Yellow bars indicate participants PCR-tested within period (right axis), Blue line indicates participants with positive PCR within period (per 1,000) (left axis). (Find accessible data used in this graph in underlying data). *Incomplete week (14 June to 20 June 2021). Please note that Figure 9 contains only participants with at least 1 PCR test within given period; participants are counted as positive if at least 1 PCR test within given period is positive. Data has not been restricted by antibody status nor vaccination status; includes only participants from trusts in England. 0 5 10 15 20 25 30 11 Jan 25 Jan 08 Feb 22 Feb 08 Mar 22 Mar 05 Apr 19 Apr 03 May 17 May 31 May 14 Jun* 0 5000 10000 15000 20000 25000 Participants with positive PCR test within period (per 1,000) 14 days beginning Participants PCR tested within period SARS-CoV-2 variants of concern and variants under investigation 33 Figure 11. Monthly frequency of potential reinfection events within SIREN. Data up to 13 June 2021. (Find accessible data used in this graph in underlying data). Of the SIREN cohort, 9,813 (31%) had evidence of prior infection (previous PCR positive or antibody positive) at enrolment. This number has increased during follow-up as participants move from the negative to positive cohort after a primary infection. From 18 June 2020 to 13 June 2021, there were 249 potential reinfections (blue line) identified in England. This is provisional data as potential reinfection cases flagged are undergoing further investigation, and some may subsequently be excluded. There were 10 potential reinfection events from April to 13 June 2021, 9 of which occurred at least 14 days after participants received their second vaccine dose. 0 10 20 30 40 50 60 70 80 90 Jun-20 Jul-20 Aug-20 Sep-20 Oct-20 Nov-20 Dec-20 Jan-21 Feb-21 Mar-21 Apr-21 May-21 Jun-21 Number of reinfection events within period Months SARS-CoV-2 variants of concern and variants under investigation 34 Variants linked to suspected SARS-CoV-2 outbreaks Data on all new acute respiratory infection (ARI) incidents reported to Health Protection Teams (HPTs) and entered on the Case and Incident Management System (CIMS) in the previous reporting week are published in the weekly influenza and COVID-19 surveillance report. This section includes information on a subset of these incidents – those suspected SARSCoV-2 clusters and outbreaks that have at least one confirmed variant of concern or variant under investigation case identified and linked to them. Incidents are assigned a variant type through an automated data linkage process which brings together incident data, case data and genomics data. Alpha and Delta variant incidents are not included here because these outbreaks have not been recorded in an equivalent way during the period that these variants are dominant so an accurate comparison cannot be made. Due to the dominance of Delta variant, all outbreaks reported from week 20 onwards can be attributed to Delta unless the outcome of sequencing confirms otherwise. Reporting on the number of outbreaks that have a confirmed linked Delta variant case will therefore lead to an under-estimation of the total burden of outbreaks associated with Delta. To track Delta variant incidents it is best to refer to the total number of outbreaks by setting which are reported in the weekly influenza and COVID-19 surveillance report. It is important to note that there is a time lag from the suspected outbreak being reported to PHE to genotyping and sequencing being undertaken and variant cases identified so data are provisional and likely to change in subsequent technical briefings. The data for this chart is available in underlying data. Note that: • an incident is an administrative record regarding a setting rather than an epidemiological classification and consequently complex, multi-variant incidents exist in a given setting • household outbreaks and clusters that have been misclassified as outbreaks linked to settings are excluded • suspected Alpha and Delta variant outbreaks and clusters are excluded • the incidents captured on the CIMS represent a subset of all ongoing clusters and outbreaks in England – a variety of arrangements are in place with local authorities and other stakeholders supporting HPTs, however, data may not routinely be documented on the CIMS SARS-CoV-2 variants of concern and