As the Omicron epidemic has intensified, South African’s reproduction rates have risen dramatically from below one percent to three within a matter of months. The super-strain is outpacing Delta at a rapid 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. Comparatively, the R rate of the UK is never higher than 1.6.
Omicron has caused a rapid rise in South African cases, mainly in Guateng. Guateng was the first country to alert the rest of the world on November 24, when the virus became highly evolved.
The national rate of cases rose by 35% to 11,535 last Thursday. This is a significant increase from the 8,500 reported yesterday. Within a matter of weeks, the strain has become the most dominant in the country. It is responsible for 75% of the sequenced samples.
The new strain was found to be at least twice as effective in re-infecting humans than any other variants, according to an earlier South African pre-print.
This may explain why the disease is rapidly spreading in Guateng province where 80 per cent of residents have natural immunity. It has not spread in countries that it was detected, such as the UK which took weeks to detect it. Only 25% of South Africans have been vaccinated, as opposed to 70% in Europe, the US, and UK.
Omicron’s infectiousness is unquestionable. However, it remains uncertain how it will evade vaccinations or how serious the disease it causes.
South African public health professionals and the World Health Organization insist that cases of the disease are not severe and vaccines against it should be effective despite the lack of information.
But a UK Government today warned she was ‘highly sceptical’ that this is truly the case, saying infections may only appear mild because people have immunity against other variants, unlike in the first wave.
Despite the optimistic outlook, South African hospitals admissions appear to be increasing despite being at a low level.
A large British study into booster vaccines revealed that Moderna as well as Pfizer had tripled the number of T cells in people double-jabbed. Scientists said this made it clear that boosters would provide high Omicron protection. So far, 42 confirmed cases in Britain have been reported.
Omicron will remain unknown to scientists for at least two weeks. Scientists can then isolate the virus and examine its biology, and compare it with the blood of previously-infected people.
South Africa’s data show that Omicron has taken control in Gauteng, and the R rate has shot up to above three per cent.
Figure: This graph illustrates the average percentage of test results that came back positive for South Africa in seven days and on a daily base (blue lines).
Graph: Seven-day average of South African cases across provinces. Guateng is the epicenter of Omicron waves in South Africa, where infections are on the rise.
This graph shows the seven-day average incidence of infections in South Africa’s provinces since October. Guateng saw an epidemic of Omicron waves, with more than 1,000 infections per day.
New images reveal how much Omicron has changed from the original Covid virus as well as other variations such Delta.
Graph shows: The UK Health Security Agency’s (UKHSA) most recent estimate for the R rate — the number of people someone with Covid infects — in Britain on November 19. It has been below 1.6 for the past few years in South Africa, and it is less than half of the estimate currently in South Africa.
According to experts who conducted a Government-funded study, booster vaccines that include Covid may offer protection against Omicron variant. Graph: This graph shows the number of T cells per 106 peripheral mononuclear blood cells after two doses (red bars), of AstraZeneca in patients who received Moderna and a third dose (blue bars).
Researchers are at an all-time high speed trying to determine if Omicron has a higher transmissibility and death rate than other mutant strains. They say that reliable estimates could take up to a week.
Early reports in South Africa suggest that many cases are either completely or mildly symptomatic. It is not clear if this could be because the strain may have spread to older persons, but there hasn’t been an age breakdown. It is considered mild by the WHO.
But epidemiologist Meaghan Kall, the UK Health Security Agency, formerly Public Health England, warned on Twitter, however, that data currently suggests Omicron may be ‘worse’ than Delta — although the picture is still emerging.
She stated that she was highly skeptical about the possibility of it being milder. It’s best to assume it is similar in severity as Delta… however, you will see milder symptoms than Delta because more people are immune now.
Pre-prints published yesterday indicated that Omicron had three times the chance of re-infecting people who’d had Covid previously.
South African researchers reported that 35,670 people had contracted the virus since the start of the pandemic. This was in addition to the 0.7% risk during South Africa’s Beta-fuelled Delta wave last winter, and Delta wave this summer.
However, the likelihood of getting the virus has increased to at most 2.4.
Stellenbosch University scientists, who are near Cape Town, stated that Omicron could be more effective at evading immunity than other viruses which have been suppressed.
The preprint means that the paper hasn’t been peer reviewed by any other scientists. These scientists then verify its conclusions.
Simon Clarke from Reading University, microbiologist said this data is the “first indication” that Omicron can overcome immunity to Covid.
He stated that although they could not confirm Omicron’s reinfection as a fact, the researchers were able to establish that Omicron did not cause the increase in transmission of Beta and Delta variants.
‘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 stated, “Omicron has exposed a major flaw in the argument that we should just allow the virus to spread and hope for immunity.”
Herd immunity now appears to be a distant dream. Omicron may have the ability to overcome vaccine-induced immunity. We are waiting for more information.
Paul Hunter, a University of East Anglia expert in infectious diseases said that Omicron would be capable of overcoming natural and possibly vaccine-induced immunity to some degree.
“Nevertheless, although it remains unclear what degree this is, there is no way to know if it will lead to 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. New targeted vaccines for omicron are likely to be created, but if the disease spreads as fast as it appears in South Africa, then many of us could have the illness by the time that a new vaccine is made.
The country had 51,402 Covid tests and 22.4% of those tested for the virus. For comparison 38.075 percent of Covid tests performed on the same day as last week were negative and 6.5 percent were positive.
While hospital admissions at Covid nearly tripled over a week, the number of deaths has fallen to 64%.
However, despite Omicron fears, South Africa still has far fewer Covid overall cases than the US and UK.
The Oxford University Research Platform Our World in Data shows that South Africa has 638 cases per million, compared with 638 in the UK or 257 in the US. The number of cases in South Africa is on the rise, but they have a modest start.
Prof Anne von Gottberg is a clinical microbiologist from the NICD. She revealed yesterday that this variant was behind 75% of national cases and that there’s a predominance Omicron in the country at a World Health Organization Conference.
Omicron was confirmed in five out of the nine country provinces. Omicron is expected to remain widespread in the four remaining areas that have yet to sequence positive samples. Because only a few positive samples have been sequenced, there are only 183 cases confirmed of this strain.
This variant of the virus has been detected in over 20 countries around the world and was likely spreading weeks before South Africa alerted. The Netherlands discovered the virus a week prior, and Nigeria detected its first case with a sample collected in October.
The strain was already known to be present in the UK even before scientists first noticed it last week. Nine cases were reported in Scotland by November 20, prompting speculations that the strain could have originated from the COP26 climate meeting or a Murrayfield Stadium rugby match against South Africa.