Omicron variant of Covid the dominant strain in South Africa

South African health authorities announced the detection of a new SARS-CoV-2 (SARS-2) variant of concern on 24 November. Within hours, airlinks to some European countries and the US were slammed shut on seven Southern African countries, in some cases only weeks after they had finally reopened. Whether this is an overreaction or not, it will have negative consequences for economies across Southern Africa, especially those that rely on tourism.

This is despite only South Africa and Botswana reporting cases of the Omicron variant in the region to date. The first case was detected by the Harvard HIV team in Botswana on 9 November. Within five days of its announcement from South Africa, more than a dozen countries had detected cases. Everyone is now bracing for potentially the biggest wave of infections yet. 

What is different about B.1.1.529, the Omicron variant? Although more than a dozen SARS-2 variants have arisen over the past two years, none has had anywhere close to the 50 mutations detected in Omicron. The Delta variant differed by only two mutations. Thus, some have called Omicron a whole new lineage of Covid, practically a different coronavirus. This is like a different strain of influenza where every year new genetic combinations arise, and new vaccines need to be developed. 

Although most scientists believe current vaccines will be mostly effective against SARS-2-omicron, this is not a certainty. Vaccine manufacturers are preparing to test their current vaccines against Omicron and, if they are less effective, they will launch new programmes immediately. New, more effective vaccines could be developed within three months. This is like the annual influenza vaccine development programme. 

As always, richer countries will be first in line to scoop new vaccines off the production line.

It is still too early to know everything about Omicron because it will take a month to see how virulent it is and how likely it is to make people sick or kill them. Scientists believe this variant probably originated in someone who was HIV positive but whose virus was not suppressed with antiviral drugs. That condition becomes a perfect laboratory for viral mutation and suggests the South African health department should place more focus on getting the close to 40% of people who are HIV positive and not using HIV health services onto antiretrovirals. In this pandemic era, this is more important than ever.

What is most striking about Omicron is that it appears to be five times as contagious as the Delta variant. Delta is 60% more contagious than the original Wuhan type virus. In just three days, the percentage of people testing positive for Covid tripled in Gauteng, the current centre of the Omicron sub-pandemic. Omicron is already the dominant strain in South Africa. Those who are unvaccinated and were passed over by Delta are unlikely to be so lucky with Omicron. 

Obviously, now is the time to get vaccinated immediately because the viral firestorm is spreading fast and those relying on natural immunity from a previous infection probably will not have that against the reconfigured Omicron. Vaccines are safe and highly effective in preventing serious illness and death. Scientists believe current vaccines will continue to be effective against omicron, at least against severe disease. 

Although vaccines do not prevent every infection, even vaccinated people who get infected can pass the virus to others. People who have breakthrough infections after a jab will not get as sick, or for as long, and their chance of infecting others is reduced.           

During a pandemic health crisis, many are confused by false and misleading information. Vaccination not only protects one’s own life, it also protects the health and lives of family, friends and the public. Those who do not get vaccinated perpetuate this pandemic and increase the chance of new mutant variants arising. 

For those who are already fully vaccinated, a booster shot is a wise precaution six months after getting their last jab. Vaccine antibody protection can decline up to 50% six months after initial vaccination, but a booster shot raises protective antibody levels to all-time highs, significantly improving original vaccine protection. Even though antibody protection wanes over time, the cellular component of the immune system still provides immunity against the disease, even if antibody protection has diminished.   

How dangerous is the new Omicron variant? We should know the answer to that question within a month. At this stage it is impossible to provide an accurate answer. Most cases of omicron have been in people that were unvaccinated. Many showed no symptoms. This suggests Omicron is no more dangerous or deadly than Delta. It might be less so. Virologists know that when a virus mutates to become more contagious, it often becomes less virulent at the same time. There is a trade-off. If Omicron is less deadly, it would be beneficial for it to spread widely and outcompete delta to become the most prevalent variant worldwide. That could lessen the impact of this pandemic. On the other hand, some of the 50 mutations of Omicron appear similar to those in the Beta variant that allowed it to evade aspects of both natural and vaccine induced immune responses. That could make Omicron more dangerous. But much is unknown. Scientists will soon answer these questions.

Although some believe if they have already had Covid they are immune from reinfection, that is not true. Scientists suggest naturally acquired immunity from infection is less effective than that provided though vaccination. With a virus that has so hugely mutated to be almost unrecognisable from the original, natural immunity would provide no more protection than one year’s influenza infection provides against the next year’s flu strain. 

Vaccination is safe, quick, and easy. Some people have flu-like symptoms for up to a day after their first or second jab. Some never experience any side-effects. Luckily, selenium supplements can still boost immunity and be used from the earliest sign of Covid infection to reduce the chance of more serious disease and death.

Half of those who become ill with Covid suffer an extended version of the disease called long Covid. Symptoms of the original illness can linger for months, even years. Long Covid may include a combination of several chronic conditions including mental, nervous system, muscular and cardiovascular illnesses. The most common is reduced lung capacity. Those who only suffer mild to moderate symptoms such as flu-like symptoms or pneumonia during initial acute SARS-2 infection can also have long Covid. Some cases of long Covid are debilitating. Some symptoms may last a lifetime. Vaccine hesitancy should be weighed against the potential of life-long ill health. Better to be safe today, than to be sorry for the rest of one’s life.

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Howard Armistead
Howard Armistead is an American Aids, Ebola, and Covid-19 researcher who has been HIV+ for 38 years. He is director of the Selenium Education and Research Centre in Johannesburg.

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