The estimate means that each infected person can transmit the virus to up to three other people.
Two other regions in southern England have R-rates above two, and there is also an increase in the Midlands, the Mirror reports.
However, the numbers suggest that numbers in northern hotspots are dropping.
In the South East, the rate is estimated at 2.34, according to a study by Imperial College London and Ipsos MORI, while in the South West it is 2.06.
East England also has an R-number greater than two, with experts putting it at 2.18.
The rate must remain below 1 for the number of cases to decrease.
It comes amid lower rates in the Northwest and Northeast, which are believed to have fallen to 1.21 and 0.57 respectively.
Across England, the R rate is estimated to be 1.6.
The REACT study, released today, indicates worrying trends are emerging in the south.
He said: “We previously reported that the prevalence was highest in the northern parts of England.
“While this is still the case, it is suggested that the epidemic could recede in the North East, although there are still marked increases in prevalence among the most vulnerable population aged 65 and over.
“The epidemic is now growing fastest in the Midlands and the South.
“The growth rate patterns and age distribution of cases in the south are now similar to those seen in the northern regions during the previous two cycles of this study. ”
The researchers warned the country is now at a “critical stage” and said the increase in hospitalizations and deaths are “inevitable” during the second wave.
There are now fears that the daily rate of new infections is reaching higher levels than at the start of the pandemic, with the official UK death toll currently standing at 45,675.
Infection rates have increased in all regions, the new data suggests, with 128 in 10,000 people having the virus between October 16 and 25.
The findings are based on random testing of 85,000 volunteers across the country.
In their report, the scientists warned that spread control measures must be followed in order to contain the pandemic.
He said: “The co-occurrence of high prevalence and rapid growth means that the second wave of the epidemic in England has now reached a critical stage.
“While it is possible that some of the current control measures are too recent to have fed into the data reported here, the high prevalence already achieved and the rapid acceleration means that there will inevitably be a large number of hospitalizations and deaths. resulting from the second wave.
“Whether through regional or national measures, now is the time to control the virus and bring R below 1 if we want to avoid even more hospitalizations and deaths from Covid-19.
Experts say the virus can usually be detected for 10 days after the initial infection.
Scientists estimate that around 960,000 people have the virus every day in England, with around 96,000 new infections every 24 hours.
Infection rates were highest in Yorkshire and The Humber, where 2.72% of people were infected with the virus, with the North West ranking second with 2.27%, the data shows.
The southeast currently has the lowest prevalence with around 0.55% having the virus.
The report states, “Our data from all previous cycles of our study indicates that at least half of people with a detectable virus will not report symptoms on the day of the test or the week before, therefore studies that rely solely on notification of symptoms of cases underestimate the incidence of the population. ”
Professor Paul Elliott, program director at the Imperial School of Public Health, said: “These interim results paint a worrying picture of the situation in England, where we are seeing an increase in the prevalence of infections with nationwide, what we know will lead to more hospitalizations and deaths.
“We are also seeing early signs that areas that previously had low infection rates are following trends seen in the worst affected areas of the country.
“Now more than ever, we must all work together to stop the spread of the virus and avoid overloading the health service.”
The Department of Health confirmed yesterday that the death toll from coronaviruses in the UK increased by 310, with 24,701 new infections confirmed.