Coronavirus statistical update: Omicron takes root in Hastings

We have now embarked on a new stage of the Covid-19 coronavirus – the age of the Omicron variant. This has shown itself to be the most transmissible yet, and in just a month has displaced Delta as the dominant variant, imposing itself on Hastings and East Sussex as well as nationally. But it appears to cause less severe illness, and so far local hospitals have been able to cope. Text by Russell Hall and Nick Terdre, research by Russell Hall.

Nearly 3.3 million people were estimated to test positive for coronavirus across England in the week leading up to New Year’s Eve, the Office for National Statistics infection survey found. This equates to around one in 15 people, the highest level of infection since the pandemic began. In London, one in 10 would have tested positive and in the South East one in 20.

The UK Health Security Agency (UKHSA) estimates over 95% of cases across England and the South East region are now from the Omicron variant.

During the week leading up to Christmas the new variant made up 75% of Hastings infections and 60% in Rother, the Sanger Institute estimates from its genome sequencing of residents’ PCR swab samples. Omicron has thus displaced Delta as the dominant local variant.

First detected locally in small numbers in the week ending 11 December, Omicron’s rise to dominance has been rapid, its growth looking to be one to two weeks behind London, which has become the epicentre for Covid-19 since the new variant first took hold in the UK. Analysis by the University of Tokyo points to Omicron spreading more than five times faster than Delta in the UK.

Since the first recorded UK case of Omicron was tested on 12 November in the East of England, the UKHSA estimates that on 14 December Omicron made up the majority of infections across England and the South East region and on 28 December over 95%.

Omicron milder than Delta

Analysis by the UKHSA and the University of Cambridge found the risk of presentation to emergency care or hospital admission with Omicron to be approximately half that for Delta and the risk of hospital admission from emergency departments with Omicron around one-third that for Delta.

The UKHSA warns it is important to highlight that these lower risks do not necessarily imply a reduced hospital burden over the current epidemic wave, given the higher growth rate and immune evasion seen with Omicron.

Although there is some evidence that the current vaccines are not as effective against Omicron as against Delta, being vaccinated does make a difference. According to UKHSA one vaccine dose is 52% effective against hospitalisation for Omicron four weeks after the jab. Two doses are 72% effective after two weeks, but this wanes to 52% after six months. A booster takes effectiveness to 88% after two weeks, but starts to wane after 10 weeks.

The likelihood of being hospitalised also varies considerably with age, as the chart below shows, with younger age groups much less affected than older groups.

Results from medical research labs around the globe show Omicron infects the lungs to a much lower degree than Delta but infects the nose and throat faster and more effectively. The University of Hong Kong found that Omicron replicates in the lungs 10 times less well than the original virus but 70 times faster in the throat than Delta. The speed of infection in the nose and throat may account for Omicron’s higher infectiousness.

Meanwhile Omicron’s lower severity could be explained by research at University of Glasgow and Imperial College London which has found that Omicron has switched the route of entry into human cells to favour the type of cells more commonly found in the nose and throat over those in the lungs.

Many cells in the lung carry a protein called TMPRSS2 on their surface that can help the virus gain entry to the cell using the ACE2 receptor, also found on cell surfaces. But this protein doesn’t grab on to Omicron very well. As a result, Omicron does a worse job of infecting cells in this manner than Delta. Through an alternative route, coronaviruses can also slip into cells that don’t make TMPRSS2. Higher in the airway, cells tend not to carry the protein, which might explain the evidence that Omicron is found there more often than in the lungs.

Infections rising locally

In Hastings 232 residents tested positive on 29 December and 165 in Rother, 98% and 99% respectively of the figures registered on the same day in 2020. But that was the peak day of the Alpha wave and with local infection rates currently rising fast, Omicron’s peak is yet to be reached.

Published case numbers may well underestimate the prevalence of infections. The daily data do not yet include reinfections, but according to Imperial College London the risk of reinfection with the Omicron variant is 5.4 times greater than with Delta. Again, testing has been restricted at times in recent days due to the limited availability of both PCR and lateral flow tests, implying that some new cases have gone undetected, at least for a while.

According to press reports, the sole distributor of lateral flow tests, Alliance Healthcare, closed down for four days between 25 and 28 December, having received 2.5m tests on Christmas Eve. At the time availability was already under strain due to high demand.

Recorded infection rates across East Sussex are highest in those aged 20-34, but have been rising in the most vulnerable 60+ age-group. This is in contrast to the autumn when Delta dominated and case rates were highest in schoolchildren. East Sussex schools return from their Christmas break today with 50.5% of 12-17 year-olds having had at least one jab in Hastings and 58.9% in Rother.

Hospitals braced

There were 43 Covid-19 patients in East Sussex hospitals on 28 December of which five were on mechanical ventilation. Of the 756 open East Sussex hospital adult general and acute beds 655 were occupied on 28 December, 4.8% by Covid-19 patients. Some headroom exists therefore for accommodating  higher demand from Covid-19 patients. Eleven of the 15 open adult critical care beds were occupied, five by the aforementioned Covid-19 patients on mechanical ventilation.

Recently East Sussex Healthcare NHS Trust hospitals have seen staff absences rising both due to Covid-19 illness or self-isolation and for other reasons. Staff absences are currently lower than this time last winter when the Alpha wave arrived a month earlier in the year than the Omicron wave, but are likely to increase due to Omicron’s greater transmissibility.

“Critical incidents” have already been declared at a number of NHS trusts as staffing numbers fall to levels at which the delivery of patient care is threatened.

East Sussex is seeing around 10 Covid-19 deaths registered a week, so far well below the 200 peak last winter when immunity through vaccination and prior infection was much lower with 9% of adults in England having antibodies compared to over 95% now.

Too late to act

The latest modelling projections for the government by Warwick University show that introducing measures now to control infection, as when household mixing was banned in March 2021, would be too late to affect the number of daily Covid-19 infections and the resulting hospitalisations.

In the view of some experts, bringing back compulsory mask-wearing on public transport and in shops and other indoor settings at an earlier stage could have restrained the growth in infections which have hit record levels. On 4 January 218,724 cases were recorded, passing 200,000 for the first time, and lifting the seven-day total to 1,269,878, more than 50% up on the previous seven days.

 

This article was updated by Nick Terdre on 5 January 2022.

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