Coronavirus (COVID-19): Omicron in Scotland - evidence paper

Information about the Omicron variant in Scotland.


1. Public Health Scotland

2. Highly probable and possible cases may overestimate Omicron as other variants can be characterised by S gene target failure. S gene target failure background rates in Scotland between July and October 2021 were stable and low (<1 in 1000 cases), suggesting this marker is a good proxy for Omicron..

3. UK case definitions. Confirmed case: COVID-19 variant of concern Omicron by sequencing or genotyping. Highly Probable: COVID 19 PCR positive, S Gene Target Failure (dropout) plus travel history from RSA, Botswana, Namibia, Nigeria, Eswatini, Lesotho, Zimbabwe, Angola, Zambia, Malawi, and Mozambique with specimen dates from 01 Nov 21 as confirmed by case interview (cases that are confirmed as another strain are excluded) Or COVID PCR/LFD positive contact of a confirmed case. Possible case under investigation: COVID 19 PCR positive plus S Gene Target Failure (dropout) and specimen dates from 01 Nov 21

4. Public Health Scotland

5. Public Health Scotland

6. COVID-19 variants identified in the UK - GOV.UK (

7. when processed on a widely-used PCR test (ThermoFisher TaqPath) in Scotland

8. Public Health Scotland COVID-19 & Winter Statistical Report

9. Public Health Scotland COVID-19 & Winter Statistical Report

10. Manchester University

11. Manchester University

12. Coronavirus (COVID-19): modelling the epidemic - (

13. Public Health Scotland

14. There are a relatively lower number of confirmed cases today due to a move from interim reports to routine reports via the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) pipeline, which are lagged by approximately 2 days. This lag is due to additional quality control and processing. More info on CLIMB.



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