I am aware that a lot of you are very uncertain about what to do regarding Omnicron and the different advice you have been given about vaccines, shielding, DMT usage and COVID-19 treatments and some of the terms used by the scientific and medical community. On top of this is the Infowars between public health professionals, their governments and the nefarious agents peddling misinformation and disinformation about COVID-19 and the COVID-19 vaccines. Many of you are also confused about the use of the terms mutation, variant and strain, which are often used interchangeably.
Mutation vs. Variant vs. Strain
A mutation simply means a change in the RNA message that SARS-CoV-2 uses as its genetic code. We humans use DNA. A mutation in the RNA code may not have any biological impact or it could change how the coronavirus regulates itself and the proteins it produces, i.e. mutations may cause variation in the structure and function of the virus.
Please be aware that when coronaviruses replicate themselves they are prone to making errors during the process of duplicating their viral RNA. These errors or mutations result in viruses that are similar but not exact copies of the original parental virus. The coronavirus (infectious particle) that is formed with these mutations then needs to infect a cell and replicate itself, i.e. be able to survive and reproduce itself. Its replicants or descendants are then called variants because they differ from the parent. Variants can differ from the parental virus by a single mutation or by many mutations.
Not all mutations have the same effect. A single mutation won’t necessarily change any of the building blocks or amino acids that are used for making a protein. If this is the case they are referred to as neutral mutations. However, single mutations may occur in a part of the virus RNA that causes a change in the amino acid sequence and change the structure, and possibly the function, of the protein.
If these structural changes of proteins result in distinct physical properties that then changes the behaviour of the new variant they are called a strain.
A new strain is a variant that is not only built differently due to mutations but also behaves differently, from its parent virus. These differences could involve binding to a different cell receptor, binding more strongly to a receptor, replicating more quickly, not being identified by previous immune memory responses, being transmitted by a different route or transmitting more efficiently, etc.
All strains are variants, but not all variants are strains. When a variant becomes a strain is not black-and-white and depends on the virology community coming together and saying the changes in the behaviour of this strain is affecting the spread, control and outcome of the virus that we now need to call this variant a strain. I think all variants that have changed the epidemiology of the pandemic and have broken through vaccine or natural immunity to a greater or lesser extent need to be called strains.
Omicron
Arguably the four most common SARS-CoV-2 variants should prior to the emergence of Omnicron be called strains:
1. UK or B.1.1.7 variant - alpha variant
2. South African or B.1.351 - beta variant
3. Brazilian or P1 - gamma variant
4. India or B.1.617.2 - delta variant
Saying this I have little doubt that the Botswana or B.1.1.529 variant, now called Omicron, should be identified as a strain. It has more mutations than the other SARS-CoV-2 variants, is much more infectious with an R or replication number of 5 to 6, and is not completely neutralised by pre-existing immunity. The latter applies to wild-type immunity from natural infection, i.e. getting COVID-19, immunity induced by the current generation of vaccinations and passive immunity from infused monoclonal antibodies with the exception of sotrovimab (Xevudy, GSK) and DZIF-10c. Although sotrovimab (Xevudy, GSK) is available on the NHS, DZIF-10c is still in development and being tested in clinical trials.
Please note that the oral antiviral agents that don’t work by binding to the spike protein should theoretically work against the Omicron strain. However, with the widespread use of oral antiviral agents, it is likely these will select for resistant strains. As with antibiotic usage with bacteria, we will need new antiviral agents to be developed, and potential combination therapies, to tackle future coronavirus strains in the future.
The good news is that some of the acquired immunity you have from having had COVID-19 with another variant or being vaccinated is likely to be cross-reactive and stop you from getting severe COVID-19 with the Omicron strain.
All approved vaccines provide a significant degree of protection against serious illness from Omicron. My interpretation is this occurs whether or not you have had your second, third or booster dose. However, only the mRNA vaccines (Pfizer-BionTech and Moderna), when antibodies levels are maximised by a booster, appear to be able to stop symptomatic infections.
At a population level, the AstraZeneca, Johnson & Johnson and other vaccines don’t seem to have much effect in stopping infection and hence the inevitable spread of Omicron. This is worrying in that many countries that have built their vaccine or COVID-19 prevention programs around these vaccines will see a surge in Omicron infections. I suspect what will happen is that Omnicron will now act as the world’s vaccine and may drive up herd immunity in countries with low vaccination rates. However, in countries with low background wild-type infections rate, such as Australia, New Zealand and China they will be forced to maintain lockdowns to protect their healthcare systems. In comparison, European countries such as the UK with high background seroprevalence rates, and high vaccination rates, could potentially run hot and allow Omnicron to infect large swathes of the population with a relatively controlled impact on healthcare services. I say relatively controlled impact as this will depend on how many of the unvaccinated population infected with Omnicron will get severe disease needing hospitalisation and potentially ITU admission and ventilation. At the moment this data is lacking and explains why the UK Government is procrastinating.
How really high levels of anti-SARS-CoV-2 spike protein antibodies prevent symptomatic infection with Omicron is possibly related to the affinity and the on-off rates of the antibody, when competing with the ACE-2 receptor, for binding to the receptor-binding-domain (RBD) of the spike protein. The higher antibody levels the more likely you are to have some binding the RBD the less chance you have of the virus binding to the ACE-2 receptor and infecting the cell and initiating or spreading the infections. To reiterate you only get these very high levels of antibody from the mRNA COVID-19 vaccines and it explains why the other COVID-19 vaccines are not effective against Omicron.
Please be careful the mRNA vaccines (Pfizer and Moderna) are only partially effective against Omicron, with increasing age you make less antibody and with time immunity wanes and antibody levels drop, which explains why the mRNA vaccines are only partially effective against Omicron. This is why the government is pushing for you to have your booster vaccine ASAP to get antibody levels as high as possible.
What if you can’t boost antibody levels because you are old and have immunosenescence, are on a chronic B-cell depleting therapy such as anti-CD20 (ocrelizumab, rituximab, ofatumumab) or anti-CD19 (inebilizumab), or you are taking an S1P-modulator (fingolimod, siponimod, ozanimod, ponesimod)? This question is really very relevant in the current phase of the pandemic where there is a surge in cases of COVID-19 due to Omnicron and people with MS are at high risk of being infected.
You can’t really stop these treatments due to their prolonged action and risk of rebound disease activity. The latter is a particular problem with the S1P modulators.
This is why I am being pragmatic and going back to my original advice of getting vaccinated/boosted ASAP as some immunity is better than no immunity even if it is only T-cell immunity. For example, if you are on an anti-CD20 therapy waiting weeks or months for B-cell reconstitution is going to put you at high risk of getting COVID-19 from Omicron. You have antivirals as backup therapy in case you get COVID-19. However, in the current environment, you need to make sure you maximise your own immunity to the virus. Please remain vigilant and socially distanced. Wear masks, wash your hands, make sure closed spaces you have to share with others are well ventilated and don’t forget your prehabilitation and if you can afford it purchase a pulse oximeter in case you need it. If you can’t afford to purchase a pulse oximeter make sure you have access to one in the event you get COVID-19. This advice is particularly important if you live alone as you can’t rely on symptoms to know if you are deteriorating you have to know what is happening to the oxygen levels in your blood.
If you haven’t been vaccinated or are against being vaccinated please reconsider. By April of next year, you will either have been vaccinated and avoided being infected with Omnicron, gotten Omicron and recovered or gotten the infection and have died. At some point in time, you need to make a decision. Isn’t it better to be in control rather than playing the lottery with mother nature?
The above advice is from a UK/NHS perspective and won’t apply to other countries.
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General Disclaimer: Please note that the opinions expressed here are those of Professor Giovannoni and do not necessarily reflect the positions of Barts and The London School of Medicine and Dentistry nor Barts Health NHS Trust. The advice is intended as general advice and should not be interpreted as being personal clinical advice. If you have problems please tell your own healthcare professional who will be able to help you.
Is Omicron a new variant or a new strain of SARS-CoV-2?