The return of the ONS infection survey and a likely Christmas wave

The ONS infection survey, which PCR tested tens of thousands of people each week for 3 years, was the crowning jewel of global Covid surveillance. Participants were randomly selected to be representative of the UK population and results did not depend on test availability, having symptoms, or test seeking behaviour. It was as good it got in terms of assessing how much Covid there was out there. That survey ended in March 2023, signing off with an estimated 2.7% of the population with Covid in the week ending 13 March 2023.

The survey has now returned, albeit in reduced form with PCR tests replaced with the less sensitive (but easier and cheaper) Lateral Flow Device tests. Today it published its first results from 28,000 people tested each week from 16-22 and 23-29 November. These estimates can be combined with today’s release of the latest Covid hospital admissions and the latest variant picture in the UK to get a handle on the UK’s current Covid situation.

The overall picture is that we are just coming out of a dip in prevalence with infections and hospital admissions rising, albeit from a lowish level. The UK Health Security Agency (UKHSA) have also just designated a new variant (JN.1) for surveillance. JN.1 is growing quite rapidly both here and in other countries. For instance, it currently appears to be driving a wave of infections and hospitalisations in the Paris region of France, where it is dominant. JN.1 is on course to be dominant here by Christmas and this, combined with seasonal socialising, suggests that we will experience another Covid wave over Christmas and into January.

Read on for more details of the picture in England, including of course, some charts!

ONS Winter Coronavirus (COVID-19) Infection Study

The ONS Winter Covid Survey released its first raw results today. Note that it provides estimates of the percentage of people tested who who would test positive in England, but that these estimates have not been adjusted for any biases in the sampling or the lower sensitivity of the LFD tests (i.e. not everyone who has Covid will test positive). These more detailed estimates will be published in a few weeks.

That said, the results provide a good rough estimate of just how much Covid is around at the moment and the trend in infections. The below chart shows the results for the whole of England (red bar) and then by English regions over the two weeks to the end of November (grey bars). The most recent week is shown in the darker colour.

The overall percentage of people testing positive is 1.2% in England in the week to 29 November, up from 1% the week before. The South East, East Midlands and the East of England saw the biggest increases week on week, but estimates have reasonably large uncertainty so we can’t read too much into it. Certainly the North of England and the West Midlands seem to have the lowest levels of Covid at the moment.

The actual proportion of people with Covid in England is likely to be a bit higher than 1.2% (once taking into account that LFD tests capture about 70% of infections), probably somewhere between 1.4%-1.8%. This would be entirely in line with previous troughs between waves during 2022 which bottomed out at about 1.5% of the population infected (see below).

When looking at the results by age (below), infections are highest - and increasing fastest - in 18-34 year olds. Middle aged adults have the next highest level of infections (about 1.5%) and children and those over 75 (thankfully) the lowest. It is quite plausible the the lower levels we see among the over 75s is partly due to the autumn booster campaign.

Hospital admissions with Covid in England

After weeks of declining admissions, the week to 1 December 2023 saw a modest 10% increase in admissions. This is entirely consistent with the data coming out of the ONS Infection Survey. This suggests that reported hospital admissions with Covid have remained a reasonable indicator of trends in of Covid infection, even as testing has dropped off in hospitals.

The latest variant picture in England

The UKHSA designated JN.1 as its own variant yesterday. It is an offshoot of the Omicron variant BA.2.86 (“Pirola”) which emerged in August and quickly spread across the world. BA.2.86 did not spread as fast as many (including me) feared, but its daughter JN.1 appears to have picked up some mutations which allow it to outcompete the existing variant landscape of mostly XBB Omicron variants. It is currently growing rapidly throughout Europe. We see a similar picture here in England (although perhaps growth is not quite so explosive) - see the chart below for variant share in England for the four most common variants.

JN.1 emerged here in mid-October and represents about a fifth of sequenced in England as of 2 December. It is doubling every 10-14 days or so and even if this growth slows, it is on track to become dominant in England by Christmas. It thus seems very likely that this will help drive another wave later this month and into January 2024.

Implications

We don’t know how big the wave will get, given various competing pressures. On the downside is the prospect of a lot of indoor mixing over the festive season and waning immunity among almost everyone under the age of 65. On the upside is the recent booster campaign protecting the majority of over 65s, plus some population immunity conferred by the wave England experienced in September and October this year. The vaccine booster this year was tailored to the XBB variants, but studies have shown that it should also provide reasonable protection against BA.2.86 variants - and that should include JN.1. There is also no evidence that BA.2.86 induces more severe disease than other circulating variants. All that said, the NHS is entering winter in a fragile state and a new Covid wave could spell disaster if combined with a significant flu wave. So far, flu rates remain very low, but they have been on the increase over the last two weeks. Fingers crossed that flu does not surge and if you experience cold symptoms, please do test for Covid!