New Covid-19 strain and flu add to NHS winter pressure

A fast-growing new strain of Covid-19, coupled with the usual winter onslaught of flu and other respiratory diseases, looks set to put the NHS under pressure into the New Year. Prospects are not improved by a reduction in the vaccination offer and disappointing uptake. Text by Nick Terdre and Russell Hall, who also researched the topic and produced the graphics.

First picked up in Luxembourg on 25 August and on 18 September in the UK, the new Covid-19 strain, JN.1, has grown strongly since.

JN.1 is a member of the Omicron BA.2.86 lineage, which was the focus of attention when HOT last reported on Covid-19 in September. Also known as  BA.2.86.1.1, JN.1 is already dominating the global variant landscape, with the UK Health Security Agency (UKHSA) estimating that up to 21 November it had a weekly growth rate advantage in the UK over the circulating variant pool of 84%.

BA.2.86 currently makes up nearly two thirds of UK sampled cases and JN.1 now accounts for two thirds of these. While its growth advantage may have dropped slightly as it battles for supremacy with its 17 fast-growing BA.2.86 ancestors, siblings and cousins, it stills remains at the head of the pack.

Funky mutation

So, why is JN.1 growing so much faster than the rest of the current variant pool?

A single mutation slap bang in the middle of the spike protein, its means of entering our cells, caused one of the nearly 10,000 amino acids that the virus genome codes for to change (from the hydrophobic leucine to the uncharged serine). This makes it a bit harder for the bug to latch onto receptors on the surface of our cells, but confers an exceptional ability to evade current immunity.

A possible extra future change in the neighbouring amino acid, which other fairly successful variants have found, could restore JN.1’s cell receptor stickiness to make it more infectious.

Covid-19 on the increase

As the above interactive chart shows, the number of Covid infections was up in the week ending 13 December compared with the previous week in every England region bar the North East.

In the same period Covid infections also rose for every age group in England except 3-17 year-olds where it was virtually unchanged.

The Covid-19 Actuaries Response Group says the England R value, or average reproduction rate per infected person, as estimated from Covid-19 hospital admissions, was 1.11 on 15 December, and has been above 1, indicating growth, since late November, as hospital admissions across England rose 22% week-on-week, and 31% in the South East.

East Sussex hospitals saw the number of Covid-19 in-patients more than double week-on-week from 22 on 10 December to 55 on 17 December, and rising as JN.1 tightens its grip.

Should our local hospitals be worried?

Top A&E doctors warned on 7 December of increasing pressure on the NHS from winter viruses, pointing to rises in flu, norovirus, and RSV (respiratory syncytial virus), along with continued Covid-19 pressure.

Since winter reporting started from 20 November, NHS daily situation reports show there was one East Sussex hospital bed occupied by a flu patient on any day in December, no beds unavailable due to diarrhea, vomiting, or norovirus, but up to six paediatric beds were unavailable leading up to 17 December due to RSV-like symptoms, that now appear to be past their peak this season.

But UKHSA surveillance data shows that flu is taking off across England. Test positivity - the proportion of tests showing positive - is currently at 9%. Last year it had reached this level by mid-November, so this year’s highest NHS winter burden looks to have shifted back and looks likely to fall in early January, instead of late December as last year - just when the trade union and professional body for doctors and medical students in the UK, the British Medical Association (BMA), plans to start a six-day junior doctors’ strike on 3 January 2024, following the three-day strike which ended on 22 December.

Although this winter looks as if it will be at least as bad for the NHS as last year, with a faster growing Covid-19 strain taking a toll than at this time last year, the peak in respiratory infections is instead likely to coincide with less social mixing in January, not in the busy run-up to Christmas as last year.

Less local accountability

So if you don’t want to spoil Christmas for yourself and your loved ones, it seems sensible to take elementary precautions such as getting vaccinated if offered the choice, and using a face mask in crowded environments.

Locally we don’t seem to be paying due attention to this advice: according to the UKHSA the Hastings Covid-19 autumn booster uptake was 63.4% up to 13 December in the eligible 65+ age group, 5.4% below the England average. (In the US uptake of only 36% in its 65+ age-group prompted the Centers for Disease Control and Prevention (CDC) to warn of an urgent need to increase immunisation).

Apart from groups at particular  risk, the autumn booster in the UK is restricted to the 65+ age group anyway. And just when the risk of catching Covid and flu is on the increase, the NHS closed online vaccination bookings on 14 December. So JN.1, BA.2.86 and their brethren may find us with our defences lowered.

It’s strange timing from the health authorities. As Imperial College immunologist Prof Danny Altmann told BBC 4’s Today programme on Monday, “We would all be in a much better place if we had a wider offer and wider uptake of vaccines.”

These UKHSA figures above come from the final update posted on the coronavirus.data.gov.uk data dashboard, which has served us so well since the early days of Covid. It is to be replaced with a dashboard which provides figures at a regional rather than local level, although the scope will be widened to include other respiratory diseases. However, one can’t but help think that the reduced granularity will diminish local accountability.

Meanwhile the Office for National Statistics (ONS), in collaboration with the UKHSA, has resumed monitoring Covid-19 community infection levels in its winter Covid-19 study, with the first full data release taking place on 21 December and monitoring due to run until 3 April 2024. This study uses lateral flow device testing instead of the PCR testing employed in the survey which ended in March.

The first results show prevalence roughly tripled in the month to 13 December to reach 1 in 23 people across England and is highest in London and the South East, with the highest occurrence in those aged 18-44.

“Speed trumps perfection”

In our September article we questioned the use of superseded vaccines at the start of the autumn Covid-19 booster campaign. HOT put this to the government health minister responsible for vaccine deployment and uptake, Lewes MP Maria Caulfield.

Her reply cited the reasoning of the Joint Committee on Vaccination and Immunisation (JCVI) that “timeliness should take priority over the choice of vaccine” in bringing forward the campaign when the potential threat of BA.2.86 was looming on the horizon.

Contrary to what we have heard in evidence given to the UK Covid-19 Inquiry about our government’s tardy responses during the first year of the pandemic in some regards, the UK may now have learnt the lesson of WHO executive director, Dr Michael Ryan, who said on 13 March 2020 that “the greatest error is not to move” and that “speed trumps perfection” when it comes to dealing with highly contagious life-threatening viruses.

It’s a lesson HBC could reflect on after shutting up shop for  two weeks, with a total absence of communication, when the first national lockdown was announced on 23 March 2020, especially as on 18 March it had granted itself emergency powers and declared its community leadership role.

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