Omicron Cometh

Yet another COVID-19 strain has emerged.

WaPo (“Announcement of new virus variant alarms world, as stocks crash and flights are banned“):

A new, possibly more infectious coronavirus variant, with an unusual number of mutations, had scientists sounding the alarm Friday and countries including the United States moving to impose travel restrictions as the world feared another setback on the long road out of the pandemic.

Senior Biden administration officials announced that starting Monday, travel to the United States will be restricted from South Africa and seven other countries — Botswana, Eswatini, Lesotho, Malawi, Mozambique, Namibia and Zimbabwe. The new policy, which does not affect U.S. citizens and permanent residents, was enacted “out of an abundance of caution,” officials said, as scientists work to learn more about the new variant.

This latest variant arrives nearly two years after the first ominous warnings about a novel coronavirus that emerged from China. Now, even as the world grows increasingly weary of measures to contain the virus, this new threat is casting a shadow across holiday celebrations.

On Friday, the World Health Organization declared the mutation-laden virus a “variant of concern” after a full-day review by the group’s scientists and dubbed it the “omicron” variant, named for a Greek letter.

“This variant has a large number of mutations, some of which are concerning,” the WHO said in a statement Friday. “Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other” variants of concern.

In many ways, the virus is acting exactly as global health experts have warned it might — creating new and potentially more dangerous variants, first detected in undervaccinated parts of the world. Still, major questions remain about omicron’s origins, transmissibility, whether it might make people sicker and whether it might be able to evade vaccines or therapeutics.

“It’s early to know the effectiveness of current vaccines against the new variant,” said Bruce Gellin, a vaccine expert and chief of global public health strategy at the Rockefeller Foundation.

Scientists in South Africa convened a news conference Thursday and said they had linked omicron to an exponential rise of infections in the country. Cases have also been identified in Belgium, Botswana, Hong Kong, Israel and other countries.

Financial markets plummeted amid news of the variant, with the Dow Jones industrial average delivering its worst day of 2021 with a 905-point plunge. By the time trading stopped at 1 p.m. because of the holiday weekend, the Dow had shed about 2.5 percent, the S&P 500 had erased 2.3 percent and the tech-heavy Nasdaq had declined 2.2 percent.

The World Trade Organization postponed its first ministerial meeting in four years because of the deteriorating health situation, Reuters reported.

Britain, Canada, France, Israel and Japan began to ban or order quarantines for air passengers arriving from the southern African region. European Union countries agreed Friday to ban air travel from seven southern African countries.

“Our view is very clear,” Dana Spinant, deputy chief spokeswoman for the European Commission, said at a news conference. “We need to act very fast, we need to be vigilant, and we need to take all measures that are appropriate at this stage to prevent this virus from entering Europe.”

The virus, alas, has already entered Europe unless I missed Belgium’s relocation. The attempt to contain the spread of the virus to southern Africa is politically prudent. Anecdotally, 61 people on two flights from South Africa to Amsterdam tested positive for the new variant.

The travel bans and quarantine measures are well ahead of the WHO recommendations for governments, which are:

  • enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants.
  • submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
  • report initial cases/clusters associated with VOC infection to WHO through the IHR mechanism.
  • where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to improve understanding of the potential impacts of the VOC on COVID-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics.

Indeed, the WHO advised against these travel bans (as has Anthony Fauci).

The WHO has warned against countries hastily imposing travel restrictions, saying they should look to a “risk-based and scientific approach”.

South Africa’s Health Minister Joe Phaahla told reporters that the flight bans were “unjustified”.

“The reaction of some of the countries, in terms of imposing travel bans, and such measures, are completely against the norms and standards as guided by the World Health Organization,” he said.

Again, I understand the impulse of politicians to do what they’re doing. It not only seems like common sense but has the advantage of showing action. But the longer-term effect of this is to encourage countries to be more like China and less like South Africa: hide news of breakouts as long as possible.

Moreover, skeptical it’ll do much good. The WHO statement gives some confidence that the scientific-medical community is on top of things but not much hope for containment.

The Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) is an independent group of experts that periodically monitors and evaluates the evolution of SARS-CoV-2 and assesses if specific mutations and combinations of mutations alter the behaviour of the virus. The TAG-VE was convened on 26 November 2021 to assess the SARS-CoV-2 variant: B.1.1.529.

The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021. The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021.

This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.

My skepticism on containment comes in here:

Individuals are reminded to take measures to reduce their risk of COVID-19, including proven public health and social measures such as wearing well-fitting masks, hand hygiene, physical distancing, improving ventilation of indoor spaces, avoiding crowded spaces, and getting vaccinated.

Only 24.1% of South Africans are vaccinated, compared to 42.7% of the global population and 59.1% in the United States. And, unlike poorer countries in Africa, the issue is not supply but rather demand.

(24 Nov) South Africa has asked Johnson & Johnson (JNJ.N) and Pfizer (PFE.N) to delay delivery of COVID-19 vaccines because it now has too much stock, health ministry officials said, as vaccine hesitancy slows an inoculation campaign.

About 35% of South Africans are fully vaccinated, higher than in most other African nations, but half the government’s year-end target. It has averaged 106,000 doses a day in the past 15 days in a nation of 60 million people.

Earlier this year the programme was slowed by insufficient doses. Now deliveries have been delayed due to oversupply, making the country an outlier in the continent where most are still starved of vaccines.

[…]

South Africa’s government has been seeking to boost the rate of daily administered doses.

“There is a fair amount of apathy and hesitancy,” said Shabir Madhi, who led the clinical study for the AstraZeneca (AZN.L) COVID-19 vaccine in South Africa.

To ramp up vaccinations, the government has launched pop-up vaccination centres and sought help from community leaders. It has also opened inoculations to children aged 12 to 17.

As pretty much everyone has been saying for months, we need to do more to push the vaccine out to the developing world if we’re ever to contain this virus and stop new variants from emerging. But we can’t get 40% of Americans to take the free vaccines. And, while there are some obvious partisan effects going on here, it’s worth noting that the WHO puts the fully vaccinated rate in the European region at just 54 percent (lower than the US) and in the more prosperous EU countries at 65 percent (only somewhat higher than the US).

It’s hard to imagine a measure simpler and less inconvenient than getting a couple of shots. And, two years into this, most people are pretty much over the restrictions on their daily lives. We’re going to continue losing people in droves and simply accept it as our new normal.

FILED UNDER: General
James Joyner
About James Joyner
James Joyner is Professor and Department Head of Security Studies at Marine Corps University's Command and Staff College and a nonresident senior fellow at the Scowcroft Center for Strategy and Security at the Atlantic Council. He's a former Army officer and Desert Storm vet. Views expressed here are his own. Follow James on Twitter @DrJJoyner.

Comments

  1. JohnMcC says:

    “We’re losing people in droves and simply accept it as the new normal”.

    Truer words ain’t never been said. I’ve been reading Ian Toll’s trilogy of the WW2 Pacific campaigns. The capture of Iwo Jima was regarded as a horrible bloody fight. The death toll shook up the ’44 Presidential election. It influenced the entire command structure of the the Army & Navy in the Pacific for the remainder of the war.

    The death toll was slightly north of 6100. Over about 6 weeks. We ‘officially’ declare about 1,000 — 1,100 Americans/day to have died from Covid. An Iwo Jima every week.

    And there is no alarm except on Wall St.

    What a country.

    (Since ‘EDIT’ popped up — I’ll quote the old GI medic who mentored me: ‘There’s nothing worse than the waste of a perfectly good human being.’)

    4
  2. steve says:

    I think we should have learned that by the time you think about doing a travel ban it is too late. At best you can hope to slow it down a week or two. I guess it does have a performative aspect. If you dont do it you will take criticism.

    Steve

    5
  3. OzarkHillbilly says:

    Anecdotally, 61 people on two flights from South Africa to Amsterdam tested positive for the new variant.

    Not according to the BBC:

    Sixty-one people who arrived in Amsterdam on two flights from South Africa have tested positive for Covid-19, Dutch officials say. They have been placed in isolation at a hotel near Schiphol airport. They were among some 600 passengers held for several hours after arrival while they were tested for the virus.

    The Dutch authorities are carrying out further testing to see if there are any cases of Omicron, named on Friday as a variant of concern by the WHO.

    As of right now, it is a variant to be watched and worried about for those on the lines, but the transmissibility of this new variant is still unknown. Time will tell.

    2
  4. OzarkHillbilly says:

    @JohnMcC: Other than maybe Jesus, or Buddha, or Mohammad, there’s never been “a perfectly good human being.” Opinions vary. 😉

    2
  5. JohnMcC says:

    @OzarkHillbilly: I believe my teacher meant that a human being is an amazing artifact, extremely useful and often pleasant & interesting. I’m pretty sure he was not commenting on virtue or significance.

    1
  6. Dude Kembro says:

    @steve: Yup. But on the brightside, maybe a little omicron panic porn will spur a surge in shots and boosters?

    4
  7. OzarkHillbilly says:

    @JohnMcC: Yeah, I know, hence the wink.

  8. Sleeping Dog says:

    The other day I saw a Tumblr post to the effect that for some vague cry of freedom, American’s are willing to accept thousands of deaths due to Covid and thousands of deaths due to gun violence. We are a strange people.

    2
  9. MarkedMan says:

    @Sleeping Dog: I mentioned this before, but I’ve realized that something my father once said about the animals on his boyhood farm also applies to people. Given a crisis situation a certain number of people will do the exactly wrong thing. As he put, they will rush back into the burning barn. Given the depth of this in our nature, there isn’t anything we can do to reduce this to zero. All we can do is develop systems and structures that prevent them from stampeding enough others to cause a disaster.

  10. OzarkHillbilly says:

    @MarkedMan: All we can do is develop systems and structures that prevent them from stampeding enough others to cause a disaster.

    You mean like vaccine mandates and masking rules?

    We are so f’ed.

    2
  11. Slugger says:

    It would be interesting to see an analysis of the multiple mutations that characterize omicron. Did each mutation occur in a stepwise fashion, or did they occur simultaneously? Unraveling this would give us insight into the evolution of the original severe acute respiratory syndrome coronavirus 2 (the Covid 19 virus), and would provide evidence for understanding the origins (natural vs lab made) of the virus. To me the appearance of multiple variants, especially one with multiple mutations, is evidence of a natural process.

    1
  12. Kathy says:

    @steve:

    The travel ban that’s needed is to ban all travel. All of it. Domestic, international, all over the world. A global lockdown.

    Which will never happen.

    BioNTech claims they are working on a variant specific vaccine, which could be rolled out in 100 days. That’s nearly three and a half months. Apparently there was no Delta specific vaccine because the original protected well enough against Delta.

    In this case, if Omicron does displace Delta, I suppose the strategy in high-vaccination countries (well, kind of high anyway), will be to get the Omicron shot as a booster, even on top of prior boosters.

    By now, too, I don’t care how it looks like or what problems it causes, we need mandatory vaccination. No exceptions, except medical ones (which are very few). Specifically, no religious exemptions*. No alternatives like daily testing, either.

    I would allow one alternative: jail until the pandemic ends. Allowing, naturally, early release for those who agree to vaccination.

    I know this would be difficult to enforce.

    I also wouldn’t mind incentives. Pay everyone $100 for each shot, retroactive to those who took shots earlier, even. Whatever it takes to vaccinate at least 95% of the population above 5 years of age (For now. We’ll have shots for infants starting at six months like we do fo other diseases).

    *I do support freedom of religion, but I think most of the religious exemptions are bogus and mostly political in nature. also, there’s no religious right to endanger others.

    6
  13. MarkedMan says:

    @OzarkHillbilly: Yes. And showing up to support your local public health and school board officials, who are regularly getting toxic abuse from the trumpers and other loons. And getting out to vote in every local and state election. And, if you have a say in company policy, being a voice for a company mandate.

    Even dictatorships can’t get everyone vaccinated. We have to accept that and figure out what to do next.

    3
  14. gVOR08 says:

    @Sleeping Dog:

    The other day I saw a Tumblr post to the effect that for some vague cry of freedom, American’s are willing to accept thousands of deaths due to Covid and thousands of deaths due to gun violence. We are a strange people.

    I’ve been reading The Dawn of Everything. Fascinating book. Small example, in North America a fair number of individuals experienced living in both native and European cultures. Given a choice, a large majority chose to live in native American cultures. Anthropology and ethnography have made a lot of assumptions trying to make sense out of very sketchy information. These authors take somewhat less sketchy information and correct many of those assumptions, perhaps with new assumptions.

    The book introduced me to a term long used in anthropology but new to me, “schismogenesis“, “creation of division”. I’m currently in a chapter talking about how North American Pacific coastal tribes were sharing a common environment and similar in many ways, but highly differentiated in many aspects of culture. The idea was that a group would emphasize differences with adjacent groups.

    Our right wing seem to be almost consciously splitting themselves into a separate tribe, identifying, sometimes inventing, and exaggerating any difference between themselves and the dominant culture. A few hundred thousand dead perhaps seems a small price to pay to prove to themselves that they’re them, not us. In fact, it seems to have been made a point of differentiation. We care about the victims and the risk to ourselves so they show they’re braver and more dedicated to freedom, or something, by not caring.

    2
  15. Michael Cain says:

    @Kathy:

    BioNTech claims they are working on a variant specific vaccine, which could be rolled out in 100 days. That’s nearly three and a half months.

    Everyone remembers the statement someone blurted out early in development of the first vaccine: “Once they gave us the genome, we designed the vaccine over the weekend.”

    The reality is so different. Verify the sequencing work. Pick the piece of protein to target. Verify the mRNA that tricks cells into producing it. Verify the encapsulating lipids are compatible, and possibly change them. Lab tests of everything. Line up (possibly building) production facilities, since there are restrictions about producing multiple vaccines in one location. Manufacturing involves a sequence of batch processes and takes weeks from beginning to ready-to-ship product. In the US, there are clinical tests that have to be done even for an EUA, unless Congress changes the rules. 100 days would be amazing.

    3
  16. Just nutha ignint cracker says:

    @Dude Kembro: Wish in one hand, shpit in the other. I wonder which hand will fill up first? Hmmm…

    1
  17. Gustopher says:

    @JohnMcC:

    I’ll quote the old GI medic who mentored me: ‘There’s nothing worse than the waste of a perfectly good human being.’

    That sounds inspirational, until you realize it was likely followed by “them’s good eatin’.”

    4
  18. JKB says:

    It’s hard to imagine a measure simpler and less inconvenient than getting a couple of shots.

    A couple of shots that have increased the incidence of myocarditis and pericarditis in otherwise healthy members younger age groups when the virus is of very low risk to those without co-morbidities.

    Now there are indications that some of the bad outcomes of the vaccines may be due to injection into the blood stream so that the spiked proteins travel away from the injection site and inflame organs, such as the heart. This easily mitigated by aspirating before injection to verify the needle isn’t in a blood vessel. Aspirating is a standard part of injection training for health care workers. It simply require the drawing on the needle a bit after insertion to see if blood comes out. If so, inject elsewhere. But the US, CDC, NIH, etc. won’t impose this methodology on those giving the injections. Japan has apparently imposed the aspirating before injection requirement.

    Trivial procedure that has the possibility of mitigating bad impact of the vaccines, but a bridge to far for US public health officials.

  19. Jax says:

    I don’t know about anybody else, but none of my shots were given anywhere near a vein. In fact, none of them even got a little spot of blood that “required” a bandaid. I’ve had worse paper cuts and cuticle rips.

    6
  20. MarkedMan says:

    Is there any bigger waste of time than missing the name of the poster and starting to read a trumper trying to sound like he knows his ass from a hole in the ground?

    6
  21. Just nutha ignint cracker says:

    @JKB: Wa! You keep riding that pericarditis horse and you’re going to exhaust it.

    But the US, CDC, NIH, etc. won’t impose this methodology on those giving the injections.

    The person who did my injection claimed to be a National Guard hospital corpsperson–she had on a very convincing ID badge noting that status. I suspect that she knows how to give IM injections without hitting a blood vessel–as do the nurses at Legacy, OHSU, and other places that are giving shots in my area. Additionally, I have to assume that Safeway’s/Walgreen’s/Rite Aid’s and other pharmacies, concerned about possible liability settlements, probably have similarly trained jabbers, though I don’t know this for a fact. It’s not exactly a closely guarded secret–nor is it rocket surgery.

    1
  22. Gustopher says:

    @JKB: wow, based on your detailed explanation I think you must have real experience with these issues, or at least a deep curiosity and knowledge from a personal interest.

    Of course, you also had the same level of detail for the various categories of minor attracted people the other day…

    1
  23. JohnMcC says:

    @Gustopher: An ancient scifi movie comes to mind. A book, ‘to serve mankind’ proved to have two meanings….

  24. Richard Gardner says:

    @Gustopher:

    Hugo Award winning short story 1975 – A Boy and His Dog https://www.imdb.com/title/tt0072730/ “It’s me or the dog…. I and the dog ate good that night” (sorry, been decades since I read it, maybe missing something)

    To Serve Mankind – was a Twilight Zone episode https://www.imdb.com/title/tt0734684/

  25. Richard Gardner says:

    Meanwhile, the WHO skipped the Greek Letters Nu and Xi in the variant names because. OK, I get that Nu would get confused with new, implying something new, Nu?

    But their excuse for skipping Xi is laughable – “It is a common family name.” Only if you are the leader of China (and pronounced totally differently). I guess no hurricanes should be given Chinese names because they are all wilting flowers, inferior humans (sarc). Bring out the smelling salts.

    Whinny the Pooh is upset.

    1
  26. Gustopher says:

    @Richard Gardner: With all the “china virus” “kung flu” shit, I’m gonna say that skipping over Xi was probably a good thing.

    Alas, idiots are already claiming that it’s a hoax because omicron is an anagram of moronic. How does someone understand what an anagram is called, and still be so fucking stupid?

    2
  27. Not the IT Dept. says:

    The real message we should be getting with the constantly emerging variants is that for all our domestic vaccination efforts there needs to be a real international effort to vaccinate everyone in the world. Not (just) because it’s a good thing to do but because it’s necessary for our own health in our own country. We have the resources but we don’t have the will. Slamming our own doors shut and locking them won’t do a thing to stop a variant. Once it’s identified, then you can safely assume it’s already here.

    2
  28. Zachriel says:

    @gVOR08: The book introduced me to a term long used in anthropology but new to me, “schismogenesis“, “creation of division”.

    Something similar happens in biology. Songbirds will differentiate by song, eventually leading to speciation.
    https://www.aaas.org/news/feather-color-and-song-drive-speciation-nearly-identical-songbirds

  29. R. Dave says:

    Indeed, the WHO advised against these travel bans (as has Anthony Fauci).

    …Moreover, [I’m] skeptical it’ll do much good. The WHO statement gives some confidence that the scientific-medical community is on top of things but not much hope for containment.

    Containment isn’t the point, and the opposition to travel bans from many public health experts is just another example of the self-defeating, credibility-destroying “noble lie” approach they took with masks at the beginning of the pandemic. Ask an epidemiologist or public health expert whether the number of independent seeding events affects the speed of the initial spread when a new pathogen is introduced into a population, and their answer will be an obvious yes. It’s an utterly uncontroversial point. Then ask them whether travel bans are effective at slowing the spread of a new pathogen, and suddenly there’s all this hemming and hawing, subject changing, and goalpost moving. It’s infuriating.

    The honest answer here is that yes, imposing a travel ban on regions with a higher incidence of a new variant of concern will almost certainly slow, but not stop, the spread to other regions, the benefit being that it buys us time develop effective vaccine boosters and reduce the number of deaths from this particular event, and the cost being that it might discourage countries from self-reporting variants of concern in the future and thus increase the number of deaths overall. Public health experts should state that fact honestly and then step back and let public opinion and the politically accountable parts of the government decide what policy approach to choose.

    Now, we all know that the public and politicians will inevitably choose to prioritize short-term certainty of reduced deaths domestically over the long-term possibility of even more reduced deaths globally (or even domestically) – and frankly, I agree with that. I’m more of a liberal internationalist than most, but I’m utterly unwilling to increase the risk of my family dying from some disease now in the hopes that accepting that risk might encourage Botswana (or whoever) to be marginally more forthcoming about future outbreaks thus resulting in a net average reduction in Americans’ pandemic risk over the long term. Sorry, but frack that.