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R rate in Omicron epicentre in South Africa soars from below one to 3.5 in just weeks

The reproduction rate in the South African province at the epicentre of the Omicron outbreak has surged from below one to over three in less than a month, as the super-strain outpaces Delta at a ferocious pace.

Public Health Officials in Guateng province estimate that the R value — a key measure used to gauge how fast a wave is growing — could be as high as 3.5. For comparison, the UK’s R rate has never been above 1.6.   

The Omicron strain has triggered a meteoric rise in cases in South Africa, mostly concentrated in Guateng, since the country that first alerted the world about the highly-evolved virus on November 24. 

Nationally, cases there soared to 11,535 on Thursday marking a 370 per cent rise in a week, and up a third on around 8,500 yesterday. It has become the dominant strain in the country in little over a week since it was officially discovered, making up 75 per cent of sequenced samples.

It comes after five cases of the COVID-19 Omicron variant were confirmed in New York state yesterday with officials insisting ’this is no cause for alarm’.

That was hours after it was revealed that a Minnesota man who attended the massive Anime NYC convention late last month in Manhattan was found to have been infected with the Omicron variant.

But the World Health Organization (WHO) today revealed zero deaths around the world have been caused by the new variant. 

A pre-print from South Africa published yesterday found that the new strain is at least two-and-a-half times better at re-infecting people than all other variants. 

This could explain why it’s spreading so fast in Guateng province, where up to 80 per cent have natural immunity, and not so fast in other countries where it has been detected for weeks. Only a quarter of South Africans are vaccinated, compared to around 70 per cent in the US, UK and Europe.

‘New York State has confirmed five cases of the omicron variant,’ Governor Kathy Hochul said in a statement. ‘Let me be clear: This is not cause for alarm. We knew this variant was coming and we have the tools to stop the spread’

New York City Mayor Bill de Blasio said the geographic spread of the new positive tests suggested the variant was now undergoing unchecked 'community spread' in the city, and wasn't linked to any one event

New York City Mayor Bill de Blasio said the geographic spread of the new positive tests suggested the variant was now undergoing unchecked ‘community spread’ in the city, and wasn’t linked to any one event 

While Omicron’s infectiousness seems unquestionable, there is growing uncertainty about how well it can evade vaccines and how severe the illness it causes will be.

Public health experts in South Africa and the WHO have insisted cases are only mild and vaccines should still be highly effective against the strain, despite a lack of data. 

But UK Health Security Agency (UKHSA) epidemiologist Meaghan Kall warned that data currently suggests Omicron may be ‘worse’ than Delta — although the picture is still emerging. She said she was ‘highly sceptical’ that the strain causes milder symptoms, saying infections may only appear less severe because people have immunity against other variants, unlike in the first wave. 

And despite the optimism, hospital admissions already appear to be on the rise in South African with Thursday’s 274 up 180 per cent on last week, even though they are rising from a low base. 

Scientist won’t know the full scale of Omicron’s infectiousness, vaccine evasiveness or lethality for another two or three weeks, when they can isolate the virus in a lab and study its biology and test it against the blood of previous-infected or vaccinated people. 

Data in South Africa shows the R-rate has soared to over three per cent in recent weeks as Omicron took hold in Gauteng province

Data in South Africa shows the R-rate has soared to over three per cent in recent weeks as Omicron took hold in Gauteng province

Graph shows: The percentage of tests coming back positive in the whole of South Africa since the start of the pandemic averaged over seven days (red line) and on a daily basis (blue line)

Graph shows: The percentage of tests coming back positive in the whole of South Africa since the start of the pandemic averaged over seven days (red line) and on a daily basis (blue line)

Graph shows: The seven-day average number of cases in provinces across South Africa. Infections are spiking in Guateng (dark green line), the epicentre of the Omicron wave in South Africa

Graph shows: The seven-day average number of cases in provinces across South Africa. Infections are spiking in Guateng (dark green line), the epicentre of the Omicron wave in South Africa

Graph shows: The seven-day average number of cases per day recorded in provinces across South Africa since the end of October. Infections increased to more than 1,000 per day in Guateng (dark green line), the epicentre of the Omicron wave

Graph shows: The seven-day average number of cases per day recorded in provinces across South Africa since the end of October. Infections increased to more than 1,000 per day in Guateng (dark green line), the epicentre of the Omicron wave

New images of the Omicron variant's 32 mutations (left) were released yesterday by the Covid Genomics UK Consortium (COG-UK). They show the variant's three mutations — H655Y, N679K, and P681H, located in the lower right of the image — that could help the virus sneak into the body more easily

New images of the Omicron variant’s 32 mutations (left) were released yesterday by the Covid Genomics UK Consortium (COG-UK). They show the variant’s three mutations — H655Y, N679K, and P681H, located in the lower right of the image — that could help the virus sneak into the body more easily

Scientists are working at breakneck speed to establish whether Omicron is more transmissible and deadly than other mutant strains. But they say it could still be at least a week before reliable estimates start to emerge.

Early reports on the ground in southern Africa suggested that most cases were mild or completely asymptomatic. But there has been no age breakdown meaning it is impossible to know whether this is because the strain is simply yet to spread to older people. 

The WHO has repeatedly claimed that it is a mild strain. WHO spokesman Christian Lindmeier today told reporters in Geneva: ‘I have not seen reports of Omicron-related deaths yet. 

‘We’re collecting all the evidence and we will find much more evidence as we go along.

‘The more countries… keep testing people, and looking specifically into the Omicron variant, we will also find more cases, more information, and, hopefully not, but also possibly deaths.’

But Dr Kall said she is ‘sceptical’ about claims the new strain causes less severe disease.

Writing on Twitter, she said: ‘I am highly sceptical it could be more mild. I think the best case is it’s equivalent in severity to Delta… but you’ll see milder symptoms now, than Delta when it emerged, because many more people have immunity now.’

The man had attended in event at

New York state recorded 11,300 new COVID-19 cases on Wednesday (not included above), the highest total since April 2021. The increase comes after a case of the Omicron variant in Minnesota was tied to an anime convention held in New York City

New York state recorded 11,300 new COVID-19 cases on Wednesday (not included above), the highest total since April 2021. The increase comes after a case of the Omicron variant in Minnesota was tied to an anime convention held in New York City

A pre-print published yesterday suggested Omicron was around three times more likely to re-infect people who had Covid before.

South African researchers said there had been 35,670 reinfections since the beginning of the pandemic, and the risk of reinfection was 0.7 per cent during the country’s Beta-fuelled second wave last winter and Delta wave in the summer.

But the risk of catching the virus again has recently spiralled to at least 2.4.

Scientists from Stellenbosch University, near Cape Town, said the findings suggested Omicron was better able to evade immunity in people who had already been infected than other variants which were suppressed by immunity.

A pre-print paper means it has not yet been reviewed by other scientists, who double-check its findings.

Microbiologist at Reading University Dr Simon Clarke said the data was the ‘first indication’ that Omicron could get around immunity from previous Covid infection.

He said: ‘There are a few caveats in this work, such as not having definitively confirmed that it was indeed Omicron that was causing the reinfection, but they were able to determine that the increased transmission of Beta or Delta variants was not a result of immune evasion. 

‘There is no indication as to how this immune evasion happens, although it can be presumed to be because of decreased antibody binding to Omicron’s mutated spike protein.’

He added: ‘Omicron has blown a big hole in the controversial argument that we should simply allow the infection to spread in an attempt to create immunity. 

‘Herd immunity which now seems like nothing more than a pipe dream. We await a further indication as to whether Omicron has any ability to evade vaccine induced immunity.’ 

Covid booster jabs ARE likely to protect against Omicron, scientists say

Covid booster vaccines are likely to offer good protection against the Omicron variant, experts behind a major new study say — in the first glimmer of hope since the emergence of the super-strain last week. 

T-cells are thought to provide longer lasting and broader protection than antibodies which deliver an initial higher boost of protection but also see that defence fade faster over time.   

Professor Saul Faust, trial lead and director of the NIHR Clinical Research Facility at University Hospital Southampton in the UK said: ‘Even though we don’t properly understand its relation to long-term immunity, the T cell data is showing us that it does seem to be broader against all the variant strains, which gives us hope that a variant strain of the virus might be able to be handled, certainly for hospitalisation and death if not prevention of infection, by the current vaccines.’

He said T cell response was not just focused on the spike protein but ‘are recognising a much broader range of antigens that might… be common to all of the variants.’

Asked specifically about Omicron, he said: ‘Our hope as scientists is that protection against hospitalisation and death will remain intact.’  

Infectious diseases expert at the University of East Anglia Professor Paul Hunter said: ‘The implications of this paper are that Omicron will be able to overcome natural and probably vaccine induced immunity to a significant degree. 

‘But, the degree is still unclear though it is doubtful that this will represent complete escape.’

He added: ‘It remains the case that the extra value of the booster vaccination dose remains the most important step that we can take to reduce the probability of severe disease. 

‘I suspect new targeted vaccinations will be developed against omicron but it the infection spreads globally as rapidly as it seems to be taking off in South Africa then most of us may already have had the infection by the time a new vaccine is available.’

Some 51,402 people in the country took a Covid test and 22.4 per cent of them tested positive for the virus. For comparison, 38,075 per cent of tests taken on the same day last week and 6.5 per cent were positive.

Meanwhile, Covid hospital admissions nearly tripled in a week, but deaths have fallen 64 per cent.

But despite fears about Omicron, South Africa is still recording far fewer overall Covid cases compared to its population size than both the UK and US.

Figures from the Oxford University research platform Our World in Data show South Africa has 63 cases per million people compared to 638 in the UK and 257 in the US. Cases are rising sharply in South Africa but are starting at a low base.

Professor Anne von Gottberg, a clinical microbiologist at the NICD, revealed at a World Health Organization conference yesterday the variant was behind 75 per cent of cases nationally and it ‘does look like there is a predominance of Omicron throughout the country’.

Five of the country’s nine provinces have confirmed Omicron cases and officials expect its prevalence to be high in the remaining four areas where positive samples have not yet been sequenced. There have only been 183 confirmed cases of the strain because only a handful of positive samples are analysed for variants.

The variant has been spotted in more than 20 countries worldwide and is likely to have been spreading for weeks before South Africa raised the alarm. The Netherlands detected a case one week earlier, while Nigeria found its first case in a sample taken in October. 

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