It was discovered today that the Omicron super-mutant variant outperformed Delta and has now become South Africa’s dominant strain. This is after infection rates soared 15% in a matter of weeks.
A public health official based in Johannesburg revealed that the highly evolved virus was now behind 75 per cent of cases nationally just eight days after South Africa first raised the alarm about the strain on November 24.
Anne von Gottberg (clinical microbiologist, South Africa’s National Health Agency) said today that there was a predominance Omicron in the country.
Because only a few positive samples have been tested for variants, there has only been one confirmed case of this strain. South Africa has an average of 8,561 cases per hour, up 170% from the 566 in 2005.
Hospitalisations increased more than twice in the past two weeks from an average of 85 per day to 184. Although the virus is thought to cause mild illnesses, it was first found in young people who were not normally hospitalized with the disease.
Omicron has been confirmed in five of nine U.S. provinces. Officials expect Omicron to increase in four other areas, where there have yet not been any sequences.
Professor von Gottberg stated that scientists are concerned about Omicron cases being found in people who had previously been exposed to Covid. This is in contrast with the rate of reinfection during previous waves.
She said that although the virus is not more easily transmissible as Delta, it’s thought the severity of the disease and the need for vaccines to protect the patient should be.
It has been detected in 28 countries and spread for several weeks, before South Africa alerted. The Netherlands had detected the case a week before Nigeria, who found their first case from a October sample.
Scientists found it in Britain even before its discovery. There were nine cases of the disease in Scotland last November 20th, leading to speculation that the strain may have been imported from the COP26 climate conference in Paris or a Murrayfield Stadium match against South Africa.
Anne von Gottberg (clinical microbiologist, South Africa’s National Institute for Communicable Diseases) said that it ‘looks like there’s a predominance Omicron in the country.
Data from the National Institute for Communicable Diseases (NICD) shows 8,561 people in South Africa tested positive in the last 24 hours — increasing six-fold in a week and nearly doubling on yesterday’s number — equating to a positivity rate of 16.5 per cent. Since the outbreak of the pandemic, South Africa has seen 2.9 million cases. Covid deaths in South Africa have risen by 27% from 22 Wednesday last week to 28 today. Gauteng is where the majority of the cases occur, and it’s the most affected area.
The graph below shows how many Covid-infected South Africaans are admitted each week. The average number of people admitted to South African hospitals per day was 146. Last week saw 1,027 people being admitted to both public and private hospitals. The virus has infected 552 people, leading to an average of 226 admissions per day.
Angelique Coetzee (chair of South African Medical Association) said Omicron-infected patients had different symptoms than hers. She reported a milder, more mild infection, such as tiredness and muscle aches. However, none of them reported symptoms such as a loss in smell, taste, or breathing problems.
Prof. von Gottberg from the National Institute for Communicable Diseases, (NICD) said that 183 of 249 South African cases have been sequenced by this super strain.
Last Wednesday, 1,275 people tested positive in South Africa — marking a 3.6 per cent positivity rate.
This number rose to 4,373 Tuesday with 10.2% of the people swabbed reporting positive results.
The upward trend continued yesterday, with 8,561 testing positive — increasing six-fold in a week and nearly doubling on Tuesday’s number — equating to a positivity rate of 16.5 per cent.
Professor von Gottberg claimed that approximately 75% of the samples have been Omicron sequenced, however, there’s a slight lag due to how long it takes to gather and sequence positive results.
And the number of positive samples sequenced — when scientists examine a positive sample in a laboratory to determine what Covid strain caused an infection — in South Africa in November equate to less than one per cent of positive cases for the month.
Scientists discovered bias in Omicron sample 1 last month. This was because scientists examined positive Omicron cases that they believed were new variants and not random samples of the population.
Professor von Gottberg commented that there was a strong predominance Omicron in the country. Omicron can be identified using sequencing in at least five of the provinces where sequencing data is available.
‘And we think the other provinces were just not identifying it yet, because we don’t have specimens that have been sequenced for those provinces.’
She also warned scientists about Omicron cases among those who had previously been positive for Covid.
South Africa has a testing database that matches positive PCR and antigen tests to people so it can count reinfections — which it defines as a positive test from an individual 90 days after they first test positive.
Professor von Gottberg said: ‘We monitored these reinfections for the Beta and for the Delta waves and we didn’t see an increase in reinfection over and above what we expect when the force of infection changes, when the wave stops.
“However, Omicron is on the rise.”
‘And that sort of speaks to that fact in our population with a high seroprevalence — so where many people have that previous infection — we believe that that previous infection does not provide them protection from infection due to Omicron.
While the US and UK are recording higher rates of Omicron infection than South Africa (the epicenter of the Omicron virus), cases in these countries are increasing rapidly and have risen by up to 400% over the past week.
South Africa’s cases are unlikely to understate because it is performing far fewer tests that the UK but comparable numbers to the US.
South Africans are less likely to have received 2 doses of Covid than the US, where nearly 60% and 70% respectively.
This graph displays the week-on-week average seven-day change in Covid cases. This graph shows how cases have increased in each province of South Africa. Although it isn’t clear exactly how many Omicron cases there are, scientists say that Omicron has spread to every provincial in the country.
“However, we hope that they have protection against serious disease, hospitalizations, and even death.”
She said that the virus is not more contagious as Delta.
She said: ‘People talk about increased transmissibility, but I think in this case, this virus might be as transmissible — its own characteristics, the virus characteristics — may be very similar or slightly less than Delta in shedding or being able to be contagious.
‘However, it’s the susceptibility of the population that is greater now because previous infection used to protect against Delta and now with Omicron it doesn’t seem to be the case.
“We think vaccines will continue to protect against serious disease. We have observed a decrease in the protection of vaccines using other versions, but vaccines have always protected us from severe diseases and admissions into hospitals.
Omicron-related illness will not be as severe in vaccinated patients than it is for those with previous infection, according to Professor von Gottberg.
When asked about reports that Omicron-infected children are being admitted to hospital in South Africa, she said there are reports of youngsters being admitted, but they have an ‘uncomplicatedclinical course’ and are discharged within a few days.
It comes after a spokesperson for the WHO, speaking anonymously to Reuters, yesterday said early data suggests the mutant strain is better at infecting people than Delta, even the fully vaccinated.
However, there are no signs that current vaccines won’t be as effective at preventing death and hospitalizations.
The WHO does not specify what evidence they are referring to. However, this comment is the first hint that Omicron may not be causing as much havoc in the world as previously thought.
These comments were made after Botswana’s health ministry disclosed that it had identified 19 Omicron cases within the country, and 16 of those who had been tested had not shown any symptoms.
Acting director of Health at the Ministry of Health and Wellness Dr Pamela Smith Lawrence said that most of the 19 people infected have tested negative.
According to her, the unwell people had mild symptoms.
It is ‘unfair’ to treat Botswana as ground zero of the new variant, Dr Smith-Lawrence added.
Yesterday, Nitzan Horowitz, Israeli Health Minister, said that there is a lot of optimism about this variant. He also stated that existing vaccines are capable of protecting against serious illness caused by the super-strain.
A report from an Israeli news channel claiming that Pfizer’s jab could prevent Omicron-related symptoms was published hours later. It is 90% effective, which is slightly lower than Delta.
The Channel 12 news broadcast also claimed the super variant is just 30 per cent more infectious than Delta — much lower than initially feared.
Comparatively, Delta is 70% more infective than Alpha, which it beat earlier this year.