Omicron: What we know about the new COVID variant

A new SARS-CoV-2 variant that was first identified by scientists in South Africa on November 24, has been labelled a “variant of concern” (VOC) by the World Health Organization (WHO). Cases have been detected in a growing list of countries, including Belgium, Hong Kong, Israel, the United Kingdom, Germany and Australia.

Evidence suggests that the new Omicron (or B.1.1.529) variant may be more transmissible than the already highly transmissible Delta variant, with the European Centre for Disease Prevention and Control referencing the variant’s “immune escape potential and potentially increased transmissibility advantage compared to Delta”.

Variants of the SARS-CoV-2 virus are not unusual. The more the virus spreads, the more likely it is to mutate. Mutations arise as the virus multiplies after it infects a human host. Once inside of a person, a virus’s job is to instruct its human host’s cells to make copies of the virus that go on to infect more cells and eventually other people. As the virus rapidly multiplies its genetic material, random errors in its DNA can occur during the copying process; these are known as mutations.

Most mutations are non-viable for the virus, meaning it can actually do the virus harm; some are viable but not advantageous to the virus; but every now and again mutations that give the new virus – now known as a variant – the edge over existing variants can occur.

Mutations are far more likely to occur in people with weakened immune systems – as they are likely to take more time to clear the virus, giving it more time to multiply and mutate – and in unvaccinated people, as their immune systems are not primed by vaccines to destroy the virus quickly before it has a chance to mutate. South Africa has a relatively low vaccination rate, with only approximately 35 percent of the population fully vaccinated, and Botswana, where it is thought to have originated, has an even lower vaccination rate – due in large measure to global vaccine inequality. If Omicron did originate in Southern Africa, then this may be part of the reason why.

When scientists assess new variants before deeming them “variants of concern” they look to see whether the new mutations are likely able to do three things: make the virus resistant to the effects of the vaccines; make the virus more transmissible when compared with existing variants; make people sicker if they were to contract the new variant.

It is still too early to know for sure if Omicron can do any or all of these things, but the fact that the WHO has classified it as a variant of concern means through a comparative assessment, it has been demonstrated to be associated with one or more of the above.

The Omicron variant is characterised by 30 mutations, three small deletions and one small insertion in the spike protein – the spikes which are on the outside of the virus and help it to enter the cells; of these, 15 are in the receptor-binding domain – the part of the spikes which allow them to bind to a host receptor.

The most widely used vaccines – Pfizer, Moderna and Oxford AstraZeneca – are based only on getting our immune systems to recognise the spike protein part of the SARS-CoV-2 virus as foreign, and building up an army of immune cells directed at this part of the virus. But if the mutations in Omicron change the spike protein enough that our immune systems can no longer fully recognise it, then it may mean there is a degree of immune escape for this variant.

It may also mean that those relying on natural immunity, immunity from a previous COVID-19 infection – not something I recommend – may have cause to worry. There is some concern that the mutations that Omicron harbours may leave people who have been previously infected open to reinfection. According to the WHO, preliminary evidence suggested an increased risk of reinfection with this variant, as compared with other VOCs.

However, it is far too early to know any of this for sure. Further virology studies are needed to understand the vaccines’ effectiveness against the new variant and its effect on reinfections. The WHO has said multiple studies are under way as advisers continue to monitor the variant. It is possible Omicron will have some escape from existing immunity given by vaccines and previous infections, but the chances of it rendering previous protection useless is extremely low and it is far more likely the vaccines will continue to offer a good degree of protection even from this variant. Moderna’s Chief Executive, Stephane Bancel has gone on the record, talking to news outlets saying he does not think the COVID-19 vaccines are going to be as effective against the Omicron variant, though he did say he wasn’t sure how much of a difference there would be.

Recent surges in new infections in South Africa have raised serious concerns about increased transmissibility of the new variant, particularly in younger people. We saw how the Delta variant that was first identified in India caused a widespread rise in cases across Europe and the US, where it surpassed the Alpha variant due to its ability to bind to human host cells quicker and with more affinity. Scientists who were trying to explain the sudden surge in cases in South Africa were the first to discover the new variant. The rapid increase in cases in South Africa associated with Omicron, suggests the variant is able to outcompete Delta, a variant that is already highly transmissible.

The rise of new variants highlights the responsibility wealthy countries have in vaccinating the rest of the world as well as their own populations … Nobody is safe until everybody is safe.

According to the WHO, Omicron has been detected at faster rates than previous surges in infection, suggesting this variant may have a growth advantage. The SARS-CoV-2 virus which causes COVID-19 uses its spike protein to bind to and infect human host cells; if the mutations on the spike protein allow for quicker and stronger binding affinity than Delta, then Omicron could soon become the dominant variant wherever it is present. Once again, it is too early to know for sure and the evaluation process is ongoing, but these early signs are worrying.

There is currently no data to suggest that those who are infected with the Omicron variant suffer any different symptoms from those who were infected with previous variants. No unusual symptoms have been reported from studies in South Africa and indeed like previous variants some people who are infected with Omicron have been asymptomatic.

There are many unknowns at play right now, but scientists are working at record speed to get a better understanding of the Omicron variant and what it might mean for the pandemic.

South Africa is owed a debt of gratitude for identifying the variant and bringing it to the attention of the world, knowing the implications this would likely have for the country and others affected by this variant. The scientists and health authorities were quick to share the information about Omicron with the rest of the world, and although it meant borders and travel were shut to them, something the South African authorities were highly critical of, it also meant other scientists could get to work uncovering the much-needed information about Omicron.

It is wise for countries that have not yet seen the variant to act quickly by putting in travel restrictions and by carefully genome sequencing high-risk individuals; we are lucky in that the Omicron variant is detectable through PCR testing.

The rise of new variants highlights the responsibility wealthy countries have in vaccinating the rest of the world, as well as their own populations. The statement made famous by the director-general of the WHO, Dr Tedros Adhanom Ghebreyesus, has never rung more true: Nobody is safe until everybody is safe.

Progress report: European Medicines Agency approves Comirnaty COVID vaccine for young children

On November 25, the European Medicines Agency (EMA) recommended approval of the use of Pfizer’s Comirnaty vaccine in 5- to 11-year-olds in a bid to protect them against the effects of COVID-19. The vaccine is already approved for use in adults and children aged 12 and above.

The Comirnaty vaccine is the name given to the Pfizer-BioNTech COVID vaccine that has been developed with younger people in mind; it contains a lower dose of the original Pfizer vaccine that would be given to adults. In children from five to 11 years of age, the dose of Comirnaty will be lower than that used in people aged 12 and above (10 µg compared with 30 µg). The regimen comprises two vaccines given three weeks apart in the muscles of the upper arm.

A study published in the New England Journal of Medicine found children aged 5 to 11 who are given a low dose of the Pfizer-BioNTech mRNA vaccine produced good antibody responses with no reported serious adverse effects. However, the study included only 2,268 participants and so may not be large enough to detect very rare adverse events.

A previous, phase one study showed that 10 µg was the optimum dose in this age group, so of the 2,268 participants, 1,517 children were randomly assigned to receive this dose while 751 children received a placebo. The two doses were given three weeks apart. The trial found three cases of COVID seven days or more after the second dose in the vaccinated group, compared with 16 cases in the placebo group, giving a vaccine efficacy estimate of 90.7 percent. These initial results are promising, and the study will follow up with the children for at least two years, with more children added over time.

The most common side effects in children aged 5 to 11 are similar to those in people aged 12 and above. They include pain, redness or swelling at the site of injection, tiredness, headache, muscle pain and chills. These effects are usually mild or moderate and improve within a few days of vaccination.

The EMA will now send its recommendation to the European Commission, which will issue a final decision.

Good news: Social media features encourage people to get COVID boosters, but is it enough?

Last week, Facebook, TikTok and Instagram launched a new set of “stickers” to allow social media users to show they have had their COVID booster jab or that they intend to. Social media “stickers” are essentially glorified emojis, a way of expressing an opinion, thought or emotion. This is not the first time these social media giants have supported the vaccine campaign; stickers were previously made available for users to add to their pages showing they had been vaccinated.

People increasingly turn to social media for information and can be influenced by prominent people on these sites, the so-called “influencers”. By adding stickers in support of the vaccine programme to their pages, influencers can help other users see that vaccines are, on balance, safe and effective.

Social media companies have allowed misinformation about the vaccines and COVID to spread rapidly online and they must work harder to remove it.

However, we must not let this light touch gesture hide the fact that these companies can also do more to prevent the spread of misinformation about the vaccines online.

Much of the vaccine hesitancy we have seen during the last year can be attributed to fake news that is spread quickly on the same sites that now provide users with these stickers. As a doctor, I fully understand that the vaccines are not without side effects and, in very rare circumstances, these side effects can be serious; but the argument for having the vaccines is compelling and the scientific evidence shows that the benefits of taking up the vaccines outweigh the risks.

Facebook, Twitter, Instagram TikTok and other social media companies have allowed misinformation about the vaccines and COVID to spread rapidly online and they must work harder to remove it. Balanced debate is welcome, provided it is based on fact, but anything outside of that has no place in a world that has seen millions die from a disease for which there are effective vaccines. I, for one, feel they must do more than simply provide a set of “stickers” for the vaccinated.

Personal account: An unvaccinated pregnant woman in the clinic

One of the best things about being a general practitioner is the variety of patients who come into your clinic each day – anyone from the elderly to newborn babies. This week I was consulting with a heavily pregnant lady about a rash she had developed. The rash itself was not related to pregnancy and we were able to manage it with the use of creams. While reviewing her records, I could see she was yet to receive any of the COVID vaccines. In the UK, all pregnant women are recommended to get the vaccines. I could see she had been offered the vaccines but had declined.

When I asked why she had declined, she told me she thought about it, but was worried about the long-term effects the vaccines would have on her unborn baby. I understood why she might be concerned: the messaging about vaccines for pregnant women has been mixed from the start.

Initially, when we did not have any data on the effects of the COVID vaccines on pregnant women, we told pregnant women not to take them; we even told women to avoid getting pregnant for at least three months after having the vaccines. This was because pregnant women were excluded from the initial studies into the vaccines – something that is not unusual in medical research, often done on ethical grounds. But this is something that needs to change as it often results in us not being able to give certain treatments to pregnant women only because research on them is lacking, and not because that particular treatment is harmful to them.

I listened to the lady’s concerns – that her friends told her the vaccines were not safe for pregnant women, and that even though her midwife had suggested she take the vaccine, she didn’t feel she was at increased risk of getting COVID and would prefer not to take it.

I pondered my role here. I certainly did not want to make her feel guilty about not having the vaccines, but I did want her to make an informed choice based on scientific facts and not hearsay from friends. When I pushed her to tell me what specifically about the vaccine worried her, she became tearful. She said she just didn’t know who to believe, as she had read several scary stories on Facebook about what might happen to her baby if she took the vaccines. I listened to her concerns and asked her gently if these stories were from reputable sources. She said she didn’t know. She said she simply didn’t know what to do in the best interests of her baby.

I really felt for her. She was the victim of information overload; she wasn’t anti-vax but instead had fallen victim to information that was unlikely to be based in science.

I then asked if she wanted me to tell her about the scientific data on vaccines in pregnancy. She agreed. I informed her that since the initial studies, many pregnant women had taken the mRNA vaccines and no adverse outcomes on babies had been detected. I told her the Royal College of Obstetricians and Gynaecologists (RCOG), the UK’s governing body on obstetrics, was advising all pregnant women to take up the vaccine. I explained that catching COVID in pregnancy increased her risk of stillbirth as well as her own chances of ending up in intensive care. I went on to say that the vaccines were not completely risk-free either, and it was all about balance; but on balance, the risks of complications from COVID in pregnancy were far worse than any risks the vaccines posed.

We agreed that she would go away and think about it; I didn’t want to pressure her into making a decision. I have yet to see whether or not she takes up the vaccines, but the case did highlight the difficult position pregnant women are in. Despite being told by medical professionals that the vaccines are better than them getting COVID, many remain sceptical. Some of that is on us as medical professionals and scientists, we need to think seriously about including pregnant women in clinical trials early on, but there is a lot of finger-pointing to be done at social media companies who allow the spread of misinformation when it comes to the vaccines.

All we can do as clinicians is keep trying to give facts to people, even if that means on an individual basis. The people who spread misinformation will never know nor take responsibility for the potential harms they do; we must however continue to fight on.

Reader’s question: Will I be able to travel abroad this festive season?

This is a difficult question to answer. Had I been asked a week ago, I would have said, “Yes, most likely.” But the new Omicron variant has changed things.

The variant is cropping up in new countries and is likely to be present in many parts of the world. Until we know whether or not it causes more severe disease or evades the protection given by vaccines, those who control borders will be eager to keep it at bay.

Omicron has changed things. Foreign travel is beginning to feel risky again and the last thing you want is to get stuck somewhere or face extortionate hotel fees if you are required to isolate on arrival back to your home country.

The tightest travel restrictions are likely to be imposed on the unvaccinated. My advice would be to get vaccinated and take up the booster when offered. Not only will these keep you safe, but they also offer you your best chance of being able to travel abroad.