Covid Scotland: Where are we with Omicron cases, hospital admissions and boosters?

In the week to January 3, 105,390 Covid cases were reported in Scotland with a seven-day positivity rate (the percentage of all swab tested which produce a positive result) of 28.7 per cent. 

Both of these are all-time highs for the pandemic in Scotland: at the peak of the Delta wave in September, a total of 44,738 cases were reported over a single week; before Omicron, the positivity rate (which serves to gauge how well testing is keeping pace with demand from infection levels in the community) previously peaked at 13.3% in August.

READ MORE: Double-vaccinated 10 times more likely to be hospitalised with Covid than people given boosters

Even Public Health Scotland (PHS) acknowledges that reported infections may be an underestimate, noting yesterday that "there continues to be large volumes of tests being processed by labs" and that "this and the holiday weekend will affect turnaround times". 

But it is clear that cases are rapidly increasing, possibly as a result of festive get togethers. 

In the week leading up to Christmas Day, Scotland reported just 45,410 cases, so the latest seven-day figure represents a 132% increase on that. 

Even when cases are tracked by specimen date (the date a positive swab was submitted for testing, which irons out any blips caused by processing bottlenecks) there is a clear spike from an average of 8,400 cases per day as of Christmas Eve to 10,800 by December 28 (a 29% increase in four days).

More recent figures by specimen date will not be published by PHS until tomorrow.

Scotland was averaging over 10,800 case per day by December 28

When cases are examined by age group, the lag between infections shifting from younger to older groups is also clear. 

In the 0-59 age group, Covid cases began climbing sharply from November 27 onwards. 

However, a similar increase was not evident in the 60-plus age group - those most likely to end up in hospital due to Covid - until December 6. 

Covid cases in the over 60s began rising around December 6, compared to November 27 for the 0-59 age group

Case rates are high across the UK as a whole, but highest in Northern Ireland where two in every 100 people were confirmed to be infected after presenting for a PCR test in the seven days to December 30. 

In Scotland, where virus rates are lowest, just over one in every 100 people were known to be positive.

However, this is likely to be an underestimate. 

READ MORE: Scotland's path from lockdown to 'new normal' in 2021

According to the most recent surveillance from the Office for National Statistics - which randomly samples thousands of households a week across the UK - an estimated one in 40 people in Scotland (and in Wales and Northern Ireland) were infected in the week to December 23. 

In England the figure was one in 25. 

Scotland had the lowest 7-day virus rate per 100,000 based on specimens collected up to December 30, the most recent date for which UK figures are available

The key question is what is happening in hospitals, however.

The number of people in hospital with Covid has also risen sharply: from 524 on Christmas Eve to 1,031 by January 3 (up 97% in ten days). 

PHS data shows that Covid hospital admissions began to rise steadily from December 16 onwards - roughly 10 days after cases began rising in the over-60s age group. 

Hospital Covid admissions have been on the rise since December 16

Intensive care admissions also appear to have been rising since around December 19 (from an average of three per day to 5.4 per day by December 29), although the actual number of people in ICU with Covid on any given day has remained fairly stable - fluctuating between 33 and 42 since December 7.

What is unclear is how many "Covid patients" are people who were admitted to hospital because of the virus (ie. the infection has made them seriously ill) and how many are "incidental" cases: patients who were admitted for non-Covid treatment but then happened to test positive, reflecting the high prevalence of the virus in the community. 

NHS Grampian's head of health intelligence Jillian Evans told the BBC on Sunday that "just over 60%" of the 'Covid patients' in her region had been admitted to hospital as a result of symptomatic illness caused by the virus.

A paper by Scottish researchers published just before Christmas indicated that hospital admissions for Omicron were running around 70% below what would be expected if the virus caused equally severe disease as Delta. 

However, they cautioned that the sample size at that time was small and largely predated the potential impact of the virus spreading into older age groups. 

READ MORE: Scientists cautiously optimistic as Covdi hospital admissions 70% lower than expected

Furthermore, even "incidental" Covid cases cause major disruption to the health service as these patients have to be kept separate - both physically and in terms of staffing - from non-Covid patients. 

The other major problem for the NHS - as well as social care, which is crucial to the flow of patients out of hospital - is staff absence. 

Fully vaccinated NHS and social care staff have self-isolation exemptions if they are identified as household or close contacts of a positive case - but if they become infected themselves, they have to isolate for the full 10 days. 

According to the latest Scottish Government data, 3,316 NHS staff were absent due to Covid in the week to December 28. That exceeds the 3,298 absences at the pek of the Delta wave at the beginning of September. 

In social care, the number of care home staff absent after testing positive reached a record 462 in the week to Boxing Day - a five-fold increase in three weeks. 

Figures published by the Scottish Government on Hogmanay also show just how rapidly Omicron has taken over as the dominant Covid variant in Scotland. 

The percentage of Covid cases with the S-gene dropout (a marker for Omicron) had hit 89.4% by December 31, compared to 15.5% on December 10. 

The number of people in hospital with confirmed Omicron infections climbed from two to 91 in little over two weeks - although this only relates to the minority of cases where genotyping has been carried out to identify a specific variant. 

In reality, the vast majority of the 1000-plus patients currently in hospital with Covid will be infected with the Omicron strain.

Finally, boosters are vital to preventing avoidable Covid admissions to hospital. 

A recent UK Health Security Agency (UKHSA) report noted that 608 out of the 815 patients hospitalised with Omicron in England had not had a third vaccine dose; one in four were unvaccinated.  

The agency said boosters appear to cut the risk of being hospitalised by Omicron by around 88%, although two doses still provided comparatively high protection of 72%. 

Based on data for Scotland last updated on December 31, almost one in 10 (9%) of over-80s in Scotland are still waiting for a booster - with coverage lower in this age group than for the 60 to 79s. 

Booster dose coverage by age group

Around 35% of care home staff are yet to receive a booster, and one in 10 severely immunosuppressed individuals are still waiting. 

However, overall coverage in Scotland is ahead of the rest of the UK on first, second and third dose uptake. 

Graphic by @TravellingTabby