The Arrival of Omicron
Steve Jones
Steve Jones • Dec 02

The Arrival of Omicron

by Steve Jones

Strange things may happen to the human brain when you subject your body to international travel, and I’m on day three of jet lag, so maybe it’s just me, but I am left wishing the WHO had not chosen the Greek alphabet as the source for COVID-19 nomenclature. Oh, it all started out just fine because there were safe names like Alpha, Beta, Gamma, Delta, but now we have Omicron.

Now to be fair to the lovely people at the World Health Organisation (WHO), naming viruses is a fraught business. We used to call viruses after where they were first discovered, but predictably that led to the stigmatisation of people from those areas.  We watched this same phenomenon play out in the first phase of the COVID-19 pandemic when certain politicians attempted to shift the blame for the virus onto China, sometimes leading to outbreaks of violence, targeting anyone who looked like they might be of Asian descent.

However, viruses must be named, and while sterile uninteresting names like SARS-CoV-2 have their place, Severe Acute Respiratory Syndrome Coronavirus-2 is, after all, a bit of a mouthful. People don’t even really use SARS-CoV-2 anymore, preferring to use the name for the clinical disease it causes COrona VIrus Disease-2019 or COVID-19.

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People don’t even really use SARS-CoV-2 anymore, preferring to use the name for the clinical disease it causes COrona VIrus Disease-2019 or COVID-19.

Coronaviruses, in common with many other micro-organisms, mutate at a disturbingly high rate. These mutants aren’t different enough from the original to be considered a separate species, but they can have significant differences and need to be tracked. Under normal conditions, this is all done behind closed doors, so scientists use combinations of numbers and letters to track the mutants as they appear, spread, and decline.  

Unfortunately, nothing about COVID-19 is normal, and science is often forced into the full glare of media and public scrutiny within hours or days of discovery. So, scientists needed a nomenclature for the variants accessible to journalists and the general public alike. 

This brings me back to my original point. Omicron (or “O” to its friends) sounds like a Marvel supervillain; I can almost hear the bass-voiced voiceover guy say, “And now: the Avengers battle with Omicron the Destroyer for the future of the universe.”  

In fact, Omicron was a supervillain in Batman comics. Of course, he was – science fiction and fantasy authors have plundered the Greek alphabet as source material for their work for decades.  

More variants will evolve, and some of them will become variants of concern. It is inevitable. Every time a virus replicates its genome, there is potential for a mutation to occur. The mutation rate for Coronaviruses is approximately 0.000001 per nucleotide per replication cycle. This is an infinitesimally small number, but the way viruses replicate works against us. Each cell can probably make 1000 copies of the infectious virus before it dies, and each patient probably produces between 10,000,000,000 to 1,000,000,000,000 during an infection. Even vanishingly rare events will occur when tens of billions of virus particles are made per person. 

More variants will evolve, and some of them will become variants of concern...Most of these mutations will have either no effect or be deleterious (make the viruses less good at growing or infecting humans).

Most of these mutations will have either no effect or be deleterious (make the viruses less good at growing or infecting humans). Still, some variations will give a slight advantage to the new virus. As a result, this new form slowly replaces the old because it either grows faster, is more infectious, or evades the host immune response with greater success. It does not necessarily follow that a quicker replication or infect virus will always cause worse disease. However, it does mean it will spread faster, replacing older variants as the Delta variant did this year. Immune evasion is always a worry because we need to create new vaccines if the virus becomes too good at avoiding the current version.  

Right now, we don’t know very much about Omicron. It has undoubtedly spread quickly. Indeed, it beat me back to Canada. When I left the UK earlier this week, Canada was Omicron-free, and by the time I landed, we had identified 2 cases with a third added to the list as I was writing this piece.  This may indicate that it grows faster or infects better than the Delta variant, but we aren’t sure yet. We do know that it has 30 mutations in the S gene. Omicron has so many mutations that some diagnostic PCR tests no longer detect the S-gene – it does, however, detect and amplify the other two gene targets. Upon PCR-testing, the lack of the S gene can be a rapid indicator that someone is infected with the Omicron variant. 

The number and placement of the S-gene mutations may impact more than just PCR testing. The most significant concern is that the number of mutations will make the Omicron variant either partially or fully resistant to the vaccines currently used. Therefore, it will likely be weeks before we have enough information to understand how Omicron behaves in the population and the effectiveness of the current vaccination programmes. Fortunately, we now can make new vaccines that are both effective and safe rapidly.

However, our systems have been stretched for nearly two years now. Personnel are exhausted, and equipment and supplies are being depleted - there is undoubtedly pandemic fatigue in the global population. Right now, it feels like the light at the end of the tunnel was a train, and we could lose much of our progress. Indeed, the timing could not be worse in the Northern hemisphere. We are entering the coldest months and the holiday season is not great for infection control. The worry about what may happen has caused quick and strong reactions from politicians, including new states of emergency and border lockdowns. While it is possible this will not be required, the response in the earliest days of the pandemic has been criticised for being too weak and slow, so it is tough to get that balance right.  

Sadly, the most vulnerable people in the world will remain vulnerable.

Sadly, the most vulnerable people in the world will remain vulnerable. Developed nations will once again look after themselves and their own first and, in so doing, damn us all to repeating this cycle. Because whilst the virus can spread and grow, particularly in immunocompromised populations in the global south, new variants of concern will continue to emerge.

So, one day soon, possibly early next year, there will be a press article about how the OMEGA variant of the SARS-CoV-2 virus has evolved, and like now, we won’t know very much about how Omega will impact the pandemic. Like Omicron, it will probably emerge in sub-Saharan Africa or Southern Asia, or some remote part of South America. Somewhere, vaccine coverage is low, health care is weak, and HIV rates are high. So, whilst Omicron is the name of a comic book villain, OMEGA is the name for the end of all things.  So, I wish that the people at WHO thought things through a little more carefully.  

But even more than this, I wish that we could finally, after two years of fighting this disease, understand that this is a fight. The virus is an active participant. It won’t just sit there unchanging while we make vaccines and drugs. It will change. Like any cunning enemy, it will exploit weaknesses in our defences.  Weaknesses like vaccine hesitancy, vaccine access inequity, holding social gatherings and refusing to wear masks.  These are, as we are so often told, personal choices.  But let’s call them what they really are personal choices to succour the enemy.  So hope about this holiday season, and in 2022 we start to make better choices, or we will be giving COVID-19 the only gift it wants this year.

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Steve Jones
Steve Jones

Steve is a recovering public health scientist and academic. He is a Terry Pratchett fanatic (which explains a lot when you know him). He loves Dr. Who and can now watch almost every episode from the sofa not behind it. He has the great good fortune to be the COO of Bright and work with this amazing team. He has travelled a lot often to places with dangerous diseases. He thinks this was fun.

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