Wednesday, December 8, 2021

O Mi Cron!


November 24, one day before Thanksgiving, South African scientists notified the WHO that they had detected a new variant of SARS-CoV-2 called B.1.1.529. While using the customary PCR testing, a technician in a South African private lab had noticed that six different test samples showed an unexpected dropout in the virus’s gene sequence--a “missing snippet,” as it were. It was so unusual that they notified their boss, who, in a rare “you-gotta-see-this” moment, passed it up the chain to world-renowned South African epidemiologist Salim Abdool Karim 

Naming this strain omicron, the WHO designated it a variant of concern (VoC) because there are as many as fifty different mutations on the virus’s spike protein, some of them overlapping with the alpha, beta, gamma, and delta SARS-CoV-2 variants, and oddly enough with the common cold virus, which is in the same Coronaviridae family. These mutations are suspect for increased transmissibility of the virus, and the Covid-19 positivity rates in South Africa have correspondingly risen by 24 percent in the two weeks since the discovery of the variant. Omicron's doubling time is an astonishing 36 hours.

Eight southern African countries affected by the Biden administration travel ban
Countries affected by the Biden travel ban

Within only a couple of days of South Africa’s announcement, the Biden administration imposed a ban on travel from RSA and seven other surrounding countries. US citizens and/or their families are exempted from the ban, however. South African scientists were stunned by what appeared to be punishment for their due diligence and transparency. South Africa is one of the world’s leaders in genomic sequencing because it already has the needed infrastructure as a result of the HIV epidemic. In South Africa’s gene sequencing model, government and academic centers collaborate within a Network for Genomic Surveillance.

If it feels like you’ve seen this travel-ban movie before, it’s because you have. Eons ago in January, 2020, the former president of the United States instituted a ban on travel to the US from China, except for US citizens and their families. Impervious to anything even remotely factual, truthful, or scientific, the ex-president persisted in citing this as a prescient and wise move, even though it soon became clear that by the time the “China ban” had been imposed, the virus had already spread to Europe. This is the cockroach phenomenon: if you see one, they’re probably all over the place. The first omicron variant in the US was detected in San Francisco in a person who had recently traveled to RSA, but in the subsequent detected cases, some had no history of travel there, meaning that it had already been propagating in the US. 

Ineffective measures

The move by the Biden Administration was explained as a means of “buying time,” but it was in fact a weak rationale and a rash decision. Omicron is an equal-opportunity infector with no particular preference for US citizens versus non-citizens arriving from South Africa. As Mike Ryan, WHO’s emergencies director, put it, “. . .  Is it that some passport holders will have the virus, and some won’t? Does the virus read your passport?” UN Secretary-General António Guterres said,"We have the instruments to have safe travel. Let's use those instruments to avoid this kind of, allow me to say, travel apartheid, which I think is unacceptable. [Bolding added.]

What the US should have done is tighten the travel requirements for everyone arriving from anywhere with a combination of Covid-19 testing and quarantining. Indeed, the Biden administration has now decreased the pre-travel Covid-19 negative test period from three days to one day. They should add a Covid test on arrival at international ports of entry, which is what the Republic of Ghana does at the Kotoka International Airport for the outrageous fee of $150.

Wake-up call

Predictions are tricky, but the omicron variant seems to be more transmissible while less deadly than delta. The irony is that in the US, we haven’t even dealt satisfactorily with delta, and the SARS-CoV-2 infection rate is still a staggering 120,494 per day, primarily in unvaccinated people. This scenario is like worrying that venomous snakes will get inside the house when we already have ferocious alligators in the kitchen.

 What omicron is telling us is that no country is safe until all countries are safe. In its report, The Tony Blair Institute for Global Change warns that the present global Covid vaccine inequity is a setup for the rise of potentially more virulent Covid strains if the virus is allowed to circulate unchecked in Africa. 

Bar chart showing share of people vaccinated against Covid-19 in different parts of the world

Only 7.2 percent of the African continent is vaccinated, and at this rate, Africa could become a reservoir for variants. Notwithstanding their promises, the world’s most advanced economies have failed miserably to share vaccines with low-income countries. 


Blanket travel bans are ultimately an ineffective blunt weapon. We can’t implement a travel ban every time a new strain of the virus appears. Speaking on a WBUR Radio podcast recently, Dr. Karim  proposes steps the world’s governments and scientists can take: First, prepare for and expect emerging variants, because that’s what SARS-CoV-2 does. Second, to the extent possible, sharpen virus surveillance worldwide to detect and identify variants, and instead of reacting out of panic and fear when they emerge, countries should share information between and among themselves according to a governing set of agreed-upon rules.

This global cooperation is crucial, because SARS-CoV-2 is almost certainly here to stay and we may need a “booster” vaccine dose tweaked annually according to the virus’s profile. Another “new normal?” Probably. Just add it to masks and physical distancing.


  1. Thank you, thank you, Kwei. I have been fit to be tied over the past couple of weeks. It's bad enough that countries like South Africa have been isolated, but other southern Africa countries with no omicron at all have been lumped into the same sack. The way the whole thing has been handled is idiotic and insanely hypocritical.

  2. Thank you, thank you, Kwei. I have been fit to be tied over the past couple of weeks. It's bad enough that countries like South Africa have been isolated, but other southern Africa countries with no omicron at all have been lumped into the same sack. The way the whole thing has been handled is idiotic and insanely hypocritical.

  3. You hit the nail on the head, Kwei. Another issue that people often don't appreciate is that sub Saharan African countries don't have the resources to support their people during lockdowns, and that many rely on tourism because it's a labor intensive business. Cutting tht off, inevitably leads to more vulnerable people.
    There is, however, an another issue. There's very high vaccine hesitancy. I think that may be related to lack of trust in leaders. Unfortunately this is true even in South Africa and Botswana that currently have good leaders. South Africa isn't short of vaccines at the moment. It is short of willing arms...

  4. Yes, you're right, and Dr. Karim and his colleague brought up the vaccine hesitancy as well--some of it following the US's cue. I didn't realize that RSA has a booming flower industry that is heavily dependent on air travel for exports. That's just one example of the knock-on effect these bans have.

  5. I agree that the response to Omicron has been political, not scientific, and that in the world today there seems little hope that a unified rational approach is in the offing. We'll all be the worse for it.

  6. An interesting article on the plight of British citizens returning to the UK from South Africa:

    1. Fascinating that these quarantine horror stories aren't exclusive to low-income countries! Passengers quarantined in Accra, Ghana on arrival because of a Covid+ test also tell tales of revolting hotel and food conditions.