Only a dozen areas of England have now not recorded a single case of an offshoot of the Delta Covid variant that experts fear is even more transmissible.
One of the Government’s largest Covid surveillance programmes detected AY.4.2 in 303 of 315 local authorities in the fortnight ending October 16, the latest available.
The 12 areas where AY.4.2 was not detected in the latest fortnight were: Babergh, Burnley, Copeland, Hinckley and Bosworth, King’s Lynn and West Norfolk, Melton, Mid Suffolk, Newark and Sherwood, Oadby and Wigston, Pendle, Rushcliffe and South Holland.
Despite data showing it is still outcompeting its ancestor, some scientists are now questioning how much more transmissible than Delta the subtype really is.
Figures show it is now behind one in ten cases in the UK, up slightly from around one in 13 a fortnight ago. But the data also reveals its curve is flattening off.
Northumbria University scientists involved in variant surveillance say it is still ‘unclear’ if AY.4.2 is actually more transmissible because too little is known about its mutations.
They pointed to the ‘founder effect’ as an alternative explanation, when a strain spreads rapidly because it is the only one in a specific cluster of cases, like a school.
But Professor Francois Balloux, a geneticist and Covid commentator at University College London who was among the first to raise concerns about the variant last week, said the slower rise was ‘still compatible’ with a 10 per cent transmission advantage.
And Professor Jeffrey Barrett, who heads up Covid surveillance at the Sanger Institute, said the data was ‘consistent with a small, but real, growth advantage vs other Delta’.
The above map shows the 12 areas AY.4.2 was not detected in (white) over the two weeks to October 16, the latest available. It has spread to almost every area of England
The above chart showed AY.4.2 accounted for a slightly higher proportion of cases in the latest week — one in ten — compared to two weeks ago — one in 13. Scientists said the slow rise was still compatible with a 10 per cent transmission advantage over Delta
The above map shows AY.4.2 cases across England over the two weeks to October 16. Darker colours suggest it is making up a higher proportion of cases, while lighter colours suggest it is making up a lower proportion of cases
AY.4.2 was first detected in the UK in June, where it has gradually spread across the whole country. Experts estimate it first emerged in London or the South East, but there is no clear proof on its origin yet.
It carries two key mutations, A222V and Y145H, which both slightly alter the shape of the spike protein which the virus uses to invade cells.
Scientists claim A222V was previously seen on another variant (B.1.177) first spotted in Spain before spreading to other countries. But studies suggest it did not make the strain more transmissible, and that it was only spread by holidaymakers returning home.
There is more concern about the mutation Y145H, which slightly changes the shape of the site antibodies bind to making it harder for them to stop an infection from happening.
Scientists say this builds on mutations in Delta, and could make the subtype even more resistant to vaccines than its parent.
AY.4.2 has been recorded in more than 40 countries to date, but the UK is the only one seeing a sustained outbreak of the subtype.
It did rise to around one in 50 Covid cases in Denmark in early September, but it has now fallen again to below one in 100. Experts in the country say they are not concerned about AY.4.2.
UK health officials labelled it a ‘variant under investigation’ last week. This category is reserved for variants which are spreading in the UK that may be more transmissible or better able to evade vaccines than other mutant strains, but is a step below ‘variant of concern’ which includes Delta and Alpha.
Scientists have raised questions over whether the AY.4.2 is actually more transmissible than other Covid variants.
Dr Matthew Bashton and Dr Darren Smith, both involved in Covid surveillance at Northumbria University, have suggested it might not be as transmissible as originally thought.
In an article for scientific publication The Conversation, they wrote: ‘AY.4.2 has grown steadily in volume to the point where it now accounts for about nine per cent of UK cases in the last 28 days.
‘But whether its two mutations offer the virus a selective advantage is unclear as well.’
They added: ‘Really, it is too early to tell if this is the beginning of the next dominant lineage. Any ability it might have to escape immunity needs to be confirmed by experimental work.’
The scientists suggested the ‘founder effect’ may explain the spread of parent variant AY.4 — the most dominant Delta subtype which includes AY.4.2 — in the UK.
This is when a ‘founder’ virus is the only one present at an area where people mix such as a concert or school.
It spreads at the locations, sparking a higher number of cases compared to other mutant strains. This then leads to data suggesting it is more transmissible but in fact the rise could be because of the events.
The pair wrote: ‘Sometimes, for a certain form of a virus to dominate, it doesn’t have to be better than others — it simply needs to be in the right place at the right time.’
Professor Balloux told MailOnline updated figures from the Sanger Institute, which makes up the bulk of genomic surveillance in Britain, still suggested the variant was around 10 per cent more transmissible than Delta.
He said: ‘I feel that the most recent numbers are still compatible with a 10 per cent higher transmissibility for AY.4.2.
‘If the lineage is at 10 per cent on a given day, it would be expected to be at 11 per cent five days later.’
Professor Barrett said: ‘AY.4.2 continues slow climb in proportion: 9.7 per cent in England in our most recent two week average, just over 10 per cent if you look only at the most recent week of data.
‘Another week consistent with small, but real, growth advantage vs. other Delta.’
The most recent technical briefing from the UK Health Security Agency — which replaced the now-defunct Public Health England — also suggested it may be more transmissible.
Scientists said it appeared to have a ‘modestly increased growth rate’ compared to other variants, and was better at spreading in households than Delta.
But Professor Lawrence Young, a virologist at Warwick Medical School, told MailOnline: ‘There’s no firm evidence of increased transmissibility but it’s still early days.
‘We don’t know anything about the immunology of AY.4.2 and whether it is more resistant to vaccine-induced immunity.’