The South African Genome Surveillance Network (NGS-SA) presented the preliminary progress of its study of the omicron variant to the Health Commission of the country’s Parliament on Wednesday afternoon. They still need time to adjust the data But, in what they already consider the beginning of the fourth wave of covid-19, they assured that they are concentrating on the transmissibility and the effect on immunity that vaccines provide. “A large part of the population is obtaining immunity from vaccines or passing the disease, so it is difficult to say what the evolution will be. The genetics of omicron is completely different from delta or previous variants, “said Richard Lessels, an expert in communicable diseases. They also do not know if the incubation period remains on the average of five days that they had verified. But, Lessels said, they do have the certainty that “vaccines are the tool that can prevent the disease from being serious and requiring hospitalization.”
“We are concerned not so much with the number of mutations, but with where they are concentrated, because many of them do so in the peak protein, and specifically in key parts that are important in accessing our cells. We don’t know if the antibodies will be able to handle them, ”Lessels explained. He also pointed out that, although most of the positives of the new variant are overcoming it with mild symptoms, “it is too early to say how dangerous omicron is, because it has been detected very recently.” “We do not know if we will see more serious cases or not,” he said.
During the presentation, the expert confirmed that the omicron variant, already present in all the country’s provinces, will take over from the delta, “Which was expanding at very low levels”, and highlighted that the PCR test is capable of detecting the variant without the need for genome sequencing. “One of the three signals or targets in the PCR is negative, the other two positive, so the test continues to be positive but something different is observed. It is not possible to detect the spike gene. And that’s what happened in the Lancet laboratory in Gauteng [provincia del norte de Sudáfrica]. They found that some of the positive cases had this mark: the knockout of the gene. Something that does not happen with the delta. For this reason, with PCR we can follow the trace of this variant in real time, it is not necessary to have the complete genetic sequence, which usually takes two weeks in the laboratory ”.
The effect of the combined mutations of the omicron variant on the behavior of the virus is the great unknown. Among the data that they have been able to confirm, the following stand out: the transmissibility is higher; the vaccines, although the variant is affecting patients with the complete regimen, avoid hospitalization; the risk of reinfection is higher; the effect of the medication (Dexamethasone) is not altered because it does not treat the virus but rather calms the symptoms; And, on whether it is a more serious virus, they point out that since they have mainly infected young people between 20 and 39 years old with greater immune capacity to resist covid-19, they cannot conclude anything for the moment.
The South African National Institute of Infectious Diseases (NICD) confirmed yesterday that in November, out of 249 localized sequences, 183 were omicron. Immunity after COVID-19, the duration of which is unknown, does not offer protection against omicron.
The vaccination battle
The province of Gauteng (the most populous in the country when including the cities of Pretoria and Johannesburg) continues to be the one with the most positive cases per day, followed by KuaZulu-Natal and the Western Cape. Eight of the 15 million citizens of Gauteng have not been vaccinated and the transmission rate has gone from infecting one person to 2.3 individuals. “It is clear that young people who are not vaccinated are of great concern. We continue to send the message that getting vaccinated is important because vaccinated people are experiencing mild symptoms, “Gauteng Prime Minister David Makhura said yesterday, having established a new mantra:” Keep calm and get vaccinated. “
Using the trump card that millions of trips are expected due to the southern summer holidays and the end of the academic year that could further extend the omicron, Makhura asked the undecided and people who have only received one dose of the vaccine –700,000 people They are waiting to receive the second dose throughout the country, according to official data – that they go en masse to the vaccination points. And he announced the installation of mobile inoculation vehicles in 40 institutes throughout the province, so that young people have no excuse.
The increase in cases in Gauteng, averaging 20% more every day in the last week, is not keeping pace with the number of hospitalizations. “The analysis of the situation continues, but we are optimistic because the number of patients admitted is lower than with the same number of infections in the third wave, the same as in the age of those admitted, among whom the percentage of vaccination is lower ”Added Mary Kawonga, a member of the Makhura Advisory Committee.
The omicron variant has been detected in more than 20 countries, but South Africa and Botswana continue to accumulate 62% of the cases identified in the world. While scientists work hard to provide answers to what the omicron will mean in the coming months, South Africa – with 41.97% of the adult population vaccinated – remains calm without lowering its guard.
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