One in 90 is the equivalent of about 620,100 people having the virus in the week up to September 18.
At the peak of the second wave in early January, around one in 50 people in England were estimated to have coronavirus.
The modelling shows the biggest increase in infections between children aged two until school Year 11 with schools returning after summer earlier this month.
The percentage testing positive decreased in all other age groups except for those aged 50 to 69, where the trend was uncertain.
England’s R number has fallen slightly to between 0.8 and 1.0, the latest government figures show.
Last week, the R value - or reproduction number - was between 0.9 and 1.1
An R value between 0.8 and 1.0 means that, on average, every 10 people infected will infect between 8 and 10 other people.
Around 60 per cent of young people have already received their vaccine since it was rolled out to the age group in August.
From 6pm on Friday, the online booking service will be another way for those aged 16 and 17 in England to get a single shot of the Pfizer jab, in line with Joint Committee on Vaccination and Immunisation advice.
The NHS is due to send thousands of texts to eligible teenagers in the coming days.
In Wales, around one in 60 people are estimated to have had Covid-19 in the week to September 18, unchanged from the previous week and the highest level since the week to December 23 last year.
In Northern Ireland, the latest estimate is also one in 60, up from one in 75 in the previous week. This is slightly below the estimate of one in 40 for the week to August 20, which was the highest since current estimates began for Northern Ireland in September 2020.
For Scotland, the ONS estimates that around one in 45 people had Covid-19 in the week to September 18, unchanged from the previous week and the highest level since estimates began for Scotland in October last year.
All figures are for people in private households.