Nov 29 2021

Get Ready for Omicron

Experts knew, and had been warning, that delta was not going to be the last Greek letter to sweep across the world. The World Health Organization (WHO) tracks variants of the SARS-CoV-2 virus which causes COVID-19. They track variants of interest (VOI) which have been identified as potentially problematic, and variants of concern (VOC) which have been demonstrated to have either increased infectivity, increased illness severity, and/or evasion of preventive measures (such as vaccines or masks). These variants are given a Greek letter designation as they are added to the list. What is now called the omicron variant has been added to the list of VOC. Here’s what we know so far.

The virus appears to have originated in South Africa. Fortunately, South Africa has a robust surveillance system and labs that can grow the virus and do a whole-genome sequence. They were therefore able to identify the variant quickly and share their information with the world. This isn’t the first variant to originate in South Africa, which raises the question of why this is the case? Increased surveillance may be part of the answer, but is not able to fully explain why. Some scientists speculate that South Africa’s large population of HIV infected and inadequately treated people provide a fertile breeding ground for new variants.

Variants are caused by mutations in the virus genome, some of which may alter proteins and therefore viral functions. SARS-CoV-2 does not have a particularly high mutation rate, but because we are having a world-wide pandemic there are lots of opportunities for new mutations to occur. It’s possible that when a person has a prolonged infection the viruses in their system are under selective pressure, so any mutation that might partly evade the immune system will be favored. Those with untreated HIV have an impaired immune response. This may be just enough to provide some selective pressure but not enough to fight off the infection, creating a breeding ground for new variants.

Regardless of how it emerged, the omicron variant is especially concerning because it has many previously unseen mutations, some of which are in the spike protein. The spike protein is what gives the virus its ability to infect cells, and is also the target of the vaccines, so mutations there are especially worrisome. We do not yet know the implications of all these mutations, but probably will have a lot more information within a couple of weeks. We do know that the omicron variant is responsible for a spike in cases in South Africa, and seems to be outcompeting other variants. It therefore seems to have increased infectivity. The same was true of the delta variant, which is why it quickly dominated new infections across the world. By contrast, the mu variant was a variant of interest because it seemed to be able to partly evade the existing vaccines, but it was less infectious than delta and therefore delta continued to dominate and mu could not get a foothold.

Research is already underway to determine if the omicron variant is targeted well by existing vaccines. Researchers can grow the virus then add plasma from a vaccinated individual with high antibody titers and see to what extent the antibodies neutralize the virus. A new strain that can evade vaccines would be most concerning, essentially hitting the reset button on this pandemic. Likely, a variant that evades vaccines would likely also have a high reinfectivity rate, so even prior infectious would not be protection. Early reports are that the omicron variant does have a high reinfectivity rate, so that is something to explore. It is not yet known if the omicron variant is more deadly to those who are infected. For that we will simply have to track those who get infected.

What eventually happens in most pandemics is that new variants emerge that are more infectious, and therefore outcompete other variants, but are less deadly. This is because no single mutation is likely to make a virus both highly infectious and more deadly. Selective pressures favor more infectious viruses, not more deadly viruses, and so just by chance alone these variants are likely to wane in their deadliness. If we are lucky a variant will emerge that is infectious enough to outcompete other variants, but causes very mild disease. So far, we have not been lucky.

This is also why the omicron variant is so concerning – it has many mutations, some of which may increase infectivity while others may alter the virus in other ways, such as evading preventive measures or even causing more severe illness. Hopefully the virus will be neither more deadly or able to evade the vaccine, but that remains to be seen.

So what can we expect? At the very least, the world is likely in for another wave of COVID-19. This pandemic is not over. What can we do? In short – get F@@@ING vaccinated. Seriously – stop the politics and the pseudoscience. The vaccines work. And the booster shots increase antibody titers to levels much higher than just being fully vaccinated. Even if the omicron variant partly evades vaccines, with high enough antibody titers they can still be highly effective.

Being vaccinated also decreases the duration of illness and the ability of the virus to replicate. Therefore this reduces the probability of new variants emerging. Experts have been saying this for months – we need the vaccines in order to prevent new variants, which is the only way out of this pandemic. To those who think it is better to get infected – think again. More people getting infected without being vaccinated increases the probability of new variants. Also – this is not a benign disease, even for those at low risk. Getting infected in order to prevent infection is nonsensical.

Specifically wealthy countries need to step up their donations of vaccines to poorer countries. New variants can emerge anywhere, and we all pay the price. Further, I think the time for gentle persuasion is long over. It’s time for draconian vaccine mandates. This is a simple matter of cost-benefit. Anyone still not persuaded that vaccines are a good idea will likely never be persuaded. Our best option at this point is to make life as difficult as possible for those who refuse to get vaccinated. Their (objectively wrong) choices are killing people, hurting the economy, stressing the health-care system and wreaking havoc that will last for decades. They do not have the right to do that. This is a public health measure, and they no more have the right to oppose needed public health measures than to poison the public water supply or speed through school zones.

We now all have to get ready for omicron, and it is likely not the last Greek letter we will all become way too familiar with.

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