Should we worry about JN1? Covid’s new variant rapidly spreading in UK

A new Covid subvariant, known as JN.1, is spreading rapidly in the UK, raising questions about whether it could spur a new wave of infections.

JN.1 was originally pinpointed in the US and its share of UK Covid infections soared from virtually nothing in mid-October to 5.6 per cent on 16 November – since when it’s likely to have risen further.

And it rose five fold between 25 October and 16 November, the last day for which comprehensive data is available, according to the CovSpectrum database.

Elsewhere, JN.1 has been found to be spreading through at least 12 countries, including Iceland, Portugal, Spain, France and the Netherlands.

But while there has been is a sharp rise in the UK and elsewhere, scientists are “cautiously optimistic” that JN.1 won’t spell huge trouble – although, as usual, they stress it’s too early to say for certain and that we should keep a close eye on it.

Scientists argue that JN.1 doesn’t so far appear to be any more severe than the other subvariants currently in circulation. And they point out that overall Covid cases are still going down in the UK at the moment, making it even harder for the new subvariant to kickstart a new wave of infections.

“JN.1 is a daughter of BA.2.86 [Pirola] which is what people were getting concerned over a month or two back,” Professor Paul Hunter, of the University of East Anglia, told i – referring to the last subvariant to cause concern which didn’t end up causing significant problems.

“It [JN.1] does seem to be spreading in the UK and as of two weeks ago was responsible for about 5 per cent of infections.

“But that increase as a proportion of all infections is against a situation where total infections have been falling quite rapidly so the effective R value is probably not that much greater than 1.0 if at all,” he said.

An “R” value of 1 means that on average every person who is infected will infect one other person, meaning that the total number of infections is stable. The greater the number is above one the faster the number of infections will rise and the greater the number below one the faster they drop.

“I am not aware of any indications that it is more lethal and I doubt it would be. So I am not particularly concerned about this new variant but as ever a bit early to be definitive,” Professor Hunter said.

“Looking back at new variants for the past year or so there was always a flurry of media excitement and some academics predicting the worst, but then a couple of months later and nothing major has happened and we move on to fear about the next new variant.

“I don’t think JN.1 will be any different, though there will probably be people once more predicting Armageddon,” he said.

Professor Rowland Kao, of Edinburgh University, meanwhile, said: “I don’t think there is enough data available to tell yet [how serious JN.1 could be].

“But it seems to be not that much different from its source, so one would hope that it therefore is not sufficiently different to be a real problem.”

However, Professor Steve Griffin, of Leeds University, struck a more cautious tone.

“JN.1 seems to have one of the largest growth advantages we’ve seen for some time, ” he said, pointing out that it has a mutation which, in the Delta variant, helped the virus fuse to the body’s cells.

“As such, whilst we should be concerned about most waves, this may well cause additional problems,” he said.

JN.1 and BA.2.86 (Pirola) are very similar but differ in spike protein, although by only one mutation. The spike – which lays on the virus’s surface – is what causes the virus to infect people.

For this reason, the spike is what vaccines will target, and the US Centres for Disease Control and Prevention predicts that vaccines will work in the same way to target both variants – just as updated vaccines was an effective treatment for BA.2.86.

It is not clear yet whether JN.1 has any different symptoms from previous variants of Covid.

The emergence of JN.1, a subvariant of the Omicron variant of Covid – and fact that it is not very different from some other subvariants – continues a trend we have seen during the dominance of the Omicron variant.

The turnover of dominant variants was quite high in the early days of Covid as the original “Wuhan” strain started to mutate – giving way the Alpha, Beta and then Delta variants, with each reigning supreme as the main source of infections for a matter of weeks or months and then passing the baton.

Then, two years ago today, the first case of a new variant, known as Omicron, was announced by South Africa – followed three days later by the first infections in the UK.

Since then, Omicron has been unshakable as the dominant variant – spawning a large number of subvariants, such as BA.2.86, or Pirola, XBB.1.5 (Kraken) and XBB.1.16 (Arcturus) along with new ones that have recently been spotted in the UK and are being closely watched; JN.1 and HV.1.

And while, through various genetic mutations, these subvariants have been different enough from each other to become major sources of Covid infection in their own right, they were nonetheless far more similar to each other – and their Omicron parent – than they were to the variants that came before.

Omicron is now so entrenched in the system, a number of its subvariants are circulating side by side. This is another characteristic that sets it apart from previous variants, which tended to have a narrower range of strains doing the bulk of the infecting.

These subvariants are now so numerous and well established – and showing no sign of losing their collective dominance – that scientists say there is a good chance that Omicron will never be supplanted as the dominant variant.

This would see Omicron becoming a permanent part of life, steadily mutating like seasonal influenza.

However, in the same breath, they caution that you can never be sure about these things and that they can change quickly, so they stop short of making a firm prediction.

“We cannot exclude the possibility of a new Variant of concern but it is unlikely. Similarly we cannot exclude the possibility of a new variant able to cause significantly more serious disease but it is unlikely.

“It is likely that omicron is here to stay for quite some time but will continue to evolve,” said Professor Hunter.

Why has Omicron been so successful?

Omicron’s ability to spread fast was the result of dozens of mutations. They altered the virus’s surface, so that antibodies produced by vaccines or previous infections could not stick tightly to it and prevent the virus from invading cells.

Scientists suspect that the variant gained its new mutations while infecting a single person with a weak immune system. Immunocompromised people can only fight off some of the coronaviruses in their bodies during an infection, allowing the ones that remain to acquire mutations that can thwart the immune system.

“Omicron has been around longest as it is the most effective at transmitting itself partly because of increased intrinsic transmissibility and partly because of partial immune escape” – mutations that help it to evade immunity built up from vaccines and previous infections,” said Professor Hunter.

“But each new subvariant of omicron has had a little less advantage over its predecessors so has increasingly struggled to become dominant. Indeed for over a year now none of the waves of infection have been driven by a single new subvariant. That trend is likely to continue,” he said.

Whether this is a good or a bad thing is hard to say for sure, scientists say.

On the upside, Omicron is much less severe than Delta, the variant that came immediately before, meaning its infections are much less likely to lead to serious illness and death – although it is more infectious, so cases are likely to have been higher than they would otherwise have been.

But there is also the possibility its dominance could have prevented a milder new variant from taking hold, posing a lower risk to those infected – although this is perhaps less likely, scientists argue.

“It’s difficult to say whether this is a good or a bad thing. On the one hand it did replace Delta which caused more severe disease – hospitalisation and deaths – per infection. So I guess it is a good thing if it forced other more lethal variants,” said Professor Hunter.

“But could it be excluding variants that would cause even less severe disease? I doubt it but it’s not impossible,” he said.

Another possible benefit to the continuing dominance of Covid is that the further the virus mutates from the original Wuhan strain that vaccines were set up to tackle the less effective those vaccines are likely to be.

This means that vaccines are already less effective against Omicron – but there is a good chance they would be even less effective against a new variant which is likely to be even more different from the Wuhan variant.

“The main significance here is the mismatch between what people have been vaccinated against, and what version of the virus they are likely to encounter in their day-to-day lives,” Professor Aris Katzourakis, of Oxford University, told i.

“For example, someone who isn’t [eligible for a booster] would have received three courses of Wuhan strain – two primary and one booster – and are therefore not really fully immunised against the currently circulating strains.

“The further we go down the Omicron path, the larger the mismatch between what people are likely to encounter, and what they have been vaccinated against. Therefore their chance of contracting the virus, and the disease, will continue to increase with time,” he said.

Meanwhile, any mismatch could be even greater with a new variant. And Professor Katzourakis is perhaps slightly less sure about whether we will see one of these.

“Omicron has certainly been an incredibly successful variant, and has spawned a multitude of successful lineages that have ebbed and flowed since.

“But it is still entirely possible that we will be surprised by another variant coming from leftfield, that is currently circulating at low levels elsewhere.”

According to Professor Rowland Kao, of Edinburgh University, Omicron was probably also helped by timing.

“Because we have moved from low international movement and lots of restrictions, to higher international movement of people and few restrictions means that variants will mix more – so that means that it is less likely that a variant may emerge in an isolated geographical ‘pocket’ then spread elsewhere”.

“A very high proportion of the population have at least some past exposure resulting in immune memory – and to quite a wide variety of virus types. So it is plausible to think that it leaves less ‘room’ for a new variant to be as successful as Omicron,” he said.