Last week, we learned from virus sequencing and rapid reporting by South African scientists that there is a new variant with 50 mutations compared with the original Wuhan strain. It quickly was named Omicron and categorized as a variant of concern by the World Health Organization, a designation that hasbeen used for only four previous variants (Alpha, Beta, Gamma, Delta) among thousands of variants noted in the evolution of the Sars-CoV-2 virus.
We do know a few things about Omicron, namely its sequence and the site of its abundant mutations, far more than previous variants of concern, and some at spots in the virus RNA that may substantially affect transmission or impair our immune system (or vaccine-induced immunity) to respond. That is all theoretical, since there have been other mutation-laden variants in the past that were picked up but turned out to be void of any clinical consequence.
We also can deduce that Omicron must have originated from an immunocompromised host to have such an extensive number of mutations (from an initial Alpha variant lineage) to rapidly evolve in the person’s body. That phenomenon has been demonstrated with multiple previous cases whereby there is unrestrained virus mutations inside a person’s body due to an inadequate immune system defense. And the individual’s chronic infection subsequently transmits to other people.
The other thing we know is that there has been an outbreak in the Gauteng province in South Africa and, after Omicron was flagged for the rest of the world, more than 15 countries have confirmed new cases, predominantly from travelers but now multiple community transmissions have already been documented.
To date, the pattern of hospitalizations in Guateng is the same as with the prior waves, no worse or better. It is likely that Omicron has been around for months, but only recently was there the first sign of a sudden rise in one place. Fortunately, it was diagnosed quickly, and the rest of the world was forewarned, far better than for the previous variants of concern.
It remains unclear whether the proliferation of cases is related to high transmission, like Delta, or immune evasion, like Beta. Most likely because of the extensive mutations or what is known as “antigen drift”, it will behave more like Beta, with some immune evasion properties. The extent of that will be sorted out in the next couple of weeks by lab studies that look at the virus in culture and sera from people who are vaccinated to see how their neutralizing antibodies fare against Omicron.
But no matter the results of these lab studies and what tracking of new cases around the world show, we have all the tools to prevail over Omicron. That includes mitigation measures like masks, especially medical grade ones, physical distancing, ventilation and air filtration.
We have remarkably potent vaccines with 95% efficacy against symptomatic infections, hospitalizations and deaths. And even though these mRNA vaccines have some waning of effectiveness over five to six months, their efficacy is fully restored to 95% with a third shot (booster).
Moreover, that third shot induces remarkably high neutralizing antibodies, much higher than the second vaccine dose, and much broader activity against variants. Furthermore, the T-cell response to vaccines are far less variant sensitive than neutralizing antibodies, which puts us in good stead for fully vaccinated people to reduce the risk of severe disease.
Beyond mitigation and vaccination, we soon will have potent pills, when taken early in the first few days of a Covid infection, one with about 90% efficacy, to prevent hospitalizations and deaths. The protective benefit of pills such as Paxlovid is not expected to be affected by Omicron in any substantive way.
There are many fully validated rapid antigen tests that should be made freely available as in many other countries to help diagnose infectiousness in people with or without symptoms, which can promote early use of treatments, such as anti-Covid pills. Accordingly, we are better positioned to defend against Omicron than we would have been earlier in the pandemic. We are also probably on the cusp of developing pan-sarbecovirus vaccines, which may protect against all future variants, and just needs a global prioritized, coordinated and funded effort to accelerate the process. Yet the paramount thing holding us back is human behavior: the unwillingness and resistance to use all these tools.
Although Omicron is a source of concern, our problem now is lack of containment of Delta in the United States, with more than 90,000 new cases a day and more than 50,000 hospitalizations. We are the number one source of new infections in the world, and they are now all Delta. Had we managed to vaccinate more than 80% of our total population, as several countries have done, and used third shots to prevent any significant waning, we would have Delta contained. Our problem now is not Omicron, but rather not using the tools we have, which are getting better and better over time.
Eric Topol is the founder and director of the Scripps Research Translational Institute, professor of molecular medicine, and executive vice-president of Scripps Research