Tuesday, December 7, 2021 | Category: Eduvation Insider
Even without much air travel or aerial warfare these days, we are nonetheless living in truly “interesting” times. Alaska and Hawaii are both under blizzard warnings, while ski country is snow-less due to drought. Summer wildfires have been followed by flooding and mudslides in the Fraser Valley, volcanic eruptions in Indonesia, and a plague of scorpions in Egypt.
Not to mention the global pandemic, of course, which has been making things interesting for 22 months now, and looks like it will drag on into a third year. As the high-stakes competition between medical science and viral evolution enters a third inning, the Omicron variant has “thrown us yet another spiky curve ball” (in the words of Ed Cara, writing for Gizmodo).
Scientists won’t be able to quantify the damage Omicron can do for several weeks yet – when we’ll all be home for the winter break, and it will be far too late to prepare for our January return to campus. But already there’s plenty of evidence emerging to tell us we need to scale back our optimism…
As I mentioned in yesterday’s weekly Précis, the B.1.1.529 strain of COVID19 is driving abrupt upswings in new infections around the world, driving a fourth wave in some countries and potentially a fifth here in Canada…
At the Omicron epicentre, South Africa, daily COVID19 case counts tripled last week – and 74% of cases were Omicron. (At least, most were mild cases among young people – although 64% of the country’s population remains unvaxxed, which could bode ill for the future as it spreads. There has already been a sharp increase of hospitalizations among all age groups, particularly young children.) So far, 1,354 cases of Omicron have been confirmed in 41 countries so far, and 55,820 are suspected – and the number is rising rapidly as PHOs begin testing for it. The UK reports 246 cases of Omicron so far, and Denmark reports 183. The US has been recording more than 100,000 new cases of COVID19 each day, but almost all of them are still Delta – although Omicron has been confirmed in one-third of US states so far. New York City knows that Omicron is spreading there, after a Minnesota man caught it while attending an anime convention. (That drove the mayor to impose the strictest vax mandate requirement on private employers anywhere in the country, yesterday.) Nearly every US state already has its ICUs at 70% capacity, and in those with substantial proportions of the population unvaxxed, things could get ugly quickly as Omicron spreads.
Assume it’s Already Here
Even without Omicron, COVID19 case counts were rising in Canada thanks to lifting restrictions and dropping temperatures. But cases of Omicron have already been confirmed in BC, Alberta, Ontario and Quebec – and hundreds of other Canadians are in isolation awaiting test results. Alberta has now identified 12 cases, mostly due to international travel – but it sounds like children have been infected at home, and taken the virus to school with them.
More Cases on Campus
Since yesterday’s roundup of 6 more cases on 3 Ontario campuses last week (at Cambrian, Loyalist, and McMaster), I’ve seen a new case announced at RRC Polytechnic, a second case at Loyalist, 2 more cases at uWaterloo, and a third residence outbreak in Southwestern Ontario…
Yesterday, news broke of an outbreak in uWindsor’s Alumni Hall campus residence. Wastewater testing apparently gave early warning back on Nov 27, but now 4 students have tested positive and the local PHO has declared an outbreak. All residents of the hall are under “modified quarantine,” as the PHO is tightening restrictions on the whole city. CBC | CTV
Omicron in London
Although it doesn’t appear to be connected to the small outbreaks in residence at Fanshawe College and Western U last week, across town here in London we have a cluster of at least 30 new cases that the local PHO says likely involve Omicron, since 2 individuals in the cluster have tested positive for it after returning from Nigeria. The PHO adds that they anticipate more than 100 high-risk close contacts, all of whom will be told to quarantine regardless of their vaccination status. Young children are the majority of recent COVID19 cases in London, and this cluster has been spreading through K-12 schools and daycares. CBC | CTV | London Free Press
London used to be the premiere test market in Canada, because it so perfectly predicted how new offerings would succeed across the country. Omicron’s sudden emergence and spread here is just an early indicator for the rest of Canada, I’m sure.
Epidemiologists must consider the interaction of multiple variables to accurately calculate the future spread of disease and its impact on healthcare systems – which in turn drives PHO restrictions. These factors include transmissibility, symptom onset, viral loads, virulence, and the effective protection provided by previous infection or vaccination – as well as less predictable human behaviours like masking, distancing, and socializing indoors. The hard scientific facts will take a few weeks yet…
Solid Data Takes Time
More than 450 researchers are eager to study the Omicron variant in their labs, to gather solid quantitative measurements of the neutralizing effect of COVID19 vaccines and antibodies in recovered patients. It’s a painstaking, time-consuming process that will take 2-4 weeks to produce early results – sometime between Dec 17-31. Many labs have mice vaccinated and ready to go, but are still waiting to get Omicron samples from South Africa so they can get started. (Reduced passenger flights have created a logistical nightmare for urgent freight too.) Other labs are engineering genetic replicas of Omicron instead – but that also takes about 2 weeks. Later this month we’ll start to see “a deluge of unfiltered information – press releases, preprint servers, some people making opinions” before a scientific consensus emerges, likely in January. It may take months to gather real-world data from epidemiology reports or clinical trials. For now, as we await solid data, many experts advise that “we just have to sit tight.” Washington Post | Sydney Morning Herald | Gizmodo
But as we head into the winter holidays with ambitious plans to reopen gyms, residences, cafeterias and lecture halls at full capacity in January, there is already plenty of evidence emerging about Omicron…
Clearly More Infectious
The Omicron variant is clearly more transmissible than previous strains of COVID19, including Delta. When it exploded on the scene in South Africa, daily infection rates spiked exponentially from 300 to more than 16,000 in mere days. One-third of the 150 high school students attending a party in Denmark came away testing positive for Omicron. The fact that a fully-vaxxed Canadian could catch Omicron in a Hong Kong quarantine hotel, from a South African traveller staying in a room across the hall, suggests that it has significantly increased aerosol transmissibility. (Surveillance footage shows that the South African traveller sometimes retrieved his room service tray without wearing a mask, or wearing a valved mask that did not filter exhaled breath.) Preliminary measures of Omicron’s R0 value place it above 6, compared to 2.5 for “COVID classic” and 5 for Delta. Some studies suggest Omicron’s transmissibility may be 66% to 500% more transmissible than Delta, although all the evidence so far is based on small non-random samples. (Whatever the labs ultimately calculate, it seems clear that Omicron is significantly more infectious than Delta.) The severity of the risk is exemplified by the WHO’s move to declare Omicron a variant of concern after just 2 days, compared to the 7 months it took to name Delta, which began ravaging India in Oct 2020. The WHO says the global risk of Omicron is “very high” based on the early evidence, while the EU rates it “high to very high.”
“The emergence of the highly mutated Omicron variant underlines just how perilous and precarious our situation is.” – Tedros Adhanom Ghebreyesus, WHO director-general
Omicron is also clearly more capable of bypassing human immunity than previous variants. In South Africa, Omicron is reinfecting recovered COVID19 patients 300% more than Delta did – “substantial population-level evidence for evasion of immunity from prior infection.” I mentioned last week that 13 fully-vaxxed members of a Portugese soccer team were infected with Omicron because one player visited Africa. Likewise at least half of the 150 fully-vaxxed guests at a Christmas party in Oslo, Norway, likely came away reinfected with COVID19 after 1 person recently returned from South Africa with the Omicron variant. Two Israeli doctors reportedly became infected with the Omicron strain despite being triple-vaxxed against COVID19. A Norwegian cruiseliner heading to New Orleans detected 10 cases among its 3,000 fully-vaxxed passengers and crew. As an EU report said last week, “the currently available evidence raises serious concern that the Omicron VOC may be associated with a significant reduction in vaccine effectiveness and increased risk for reinfections.”
Risks Despite Vaccination
Add to the evidence of breakthrough infections by Omicron, the growing evidence of waning immunity for all of us who got our second dose in July or earlier, and Omicron is going to fuel plenty of breakthrough infections, even among fully-vaxxed students, staff and faculty on campus in January. Many may experience only mild symptoms, or none at all – but they will help spread COVID19 to the handful of immune-compromised or vax-exempt people on our campuses and in the surrounding community.
“It is conceivable that… the vaccines we have may well be able to contain this. Then this won’t be as serious as some people are surmising it might be.” – Anthony Fauci, director, National Institute of Allergy and Infectious Diseases
Likely to Outcompete Delta
The Omicron variant will need to consistently outcompete Delta in the wild, if it is to spread worldwide and become the dominant strain. (Previous variants of concern, like Beta and Gamma, had the potential to worsen the pandemic, but quickly faded to become mere footnotes in pandemic history.) We have no conclusive data yet, but in the worst-hit regions of South Africa, Omicron already accounts for 74% of new cases, displacing Delta. Mathematical modelling in the EU projects that Omicron could become the dominant strain there “within the next few months.”
“We have seen these mutations in other strains, in twos and threes, and each time they were a little harder to neutralize but didn’t spread particularly well. Now, all together? It’s a complete black box.” – Benjamin Neuman, virologist, Texas A&M U
Omicron is likely to drive a new wave of infections, based on all the evidence available so far. It is more infectious than Delta, capable of reinfecting recovered COVID19 patients and infective fully-vaccinated ones, and certainly appears poised to outcompete Delta and become the next dominant strain. Omicron is therefore a crucial turning point in the pandemic – but will it usher in more dark times ahead, or light at the end of the COVID19 tunnel?
UBC infectious disease specialist Horacio Bach reports that common Omicron symptoms are “completely different” from previous COVID19 variants, and include extreme fatigue, muscle pain, dry cough and throat itchiness. Yale pulmonologist Lauren Ferrante adds that reports from South Africa suggest patients experience no loss of taste or smell. (Classic COVID19 symptoms include fever/chills, cough, runny nose, headache/muscle aches, gastrointestinal issues, and loss of taste or smell.) But with the relatively small number of symptomatic Omicron cases to date, we can’t be certain: we have to wait until thousands of cases are confirmed before robust data can be gathered.
Likewise, we will need thousands of confirmed Omicron cases to measure its severity and complications – and 3 weeks or more to see its impact on hospitalizations and deaths. (Remember the “mortality lag.”) So far, Omicron cases in South Africa appear to be less severe than Delta – although that could be skewed by the fact that initial outbreaks were among otherwise healthy young university students. Of the first 70 cases reported in Europe, half had no symptoms at all, and the other half only mild symptoms. Experts have been predicting for 18 months now that COVID19 could evolve into a more benign, endemic annual virus, much like the coronaviruses that cause the common cold. (In fact, one preprint study already reports that a snippet of Omicron’s genetic code doesn’t appear in any previous COVID19 variant, but is “ubiquitous” in cold viruses.) If Omicron is less deadly and poised to become endemic, UBC evolutionary biologist Sarah Otto says we could simply “let it run its course and reach the world.” It could rapidly “train the immune system” of unvaxxed populations, almost like a vaccine. As one biostatistician observes, “if it can get around the vaccines, but in the end really causes less severe disease, that’s probably a step in the right direction.” We can hope – but as Otto also warns, “hope isn’t science.” British epidemiologist Adam Kucharski has graphed the devastating impact of a 50% less lethal strain that is 50% more transmissible (see below). And Oxford evolutionary biologist Aris Katzourakis says he “very much doubts the variant’s mutations will result in decreased severity.” National Post | National Post
“Hope isn’t science.” – Sarah Otto, evolutionary biologist, UBC
In theory, the 30+ mutations affecting Omicron’s spike protein will pose a much greater challenge to existing vaccines than did Alpha or Delta. (Three spike protein mutations in particular appeared previously in variants of concern, but this is the first time they have appeared together.) Existing COVID19 vaccines have lost some ground in preventing infection entirely from Delta, but continue to provide strong protection against severe disease – and as Oxford U points out, “there is no evidence so far that Omicron is any different.” (Of course, absence of evidence is not evidence of anything.) BioNTech’s CEO says its Pfizer vaccine will “likely” offer “substantial protection against severe disease caused by Omicron.” GlaxoSmithKline reports that its antibody treatment is effective against a bioengineered virus with some of Omicron’s mutations. But Moderna CEOStéphane Bancel startled world markets when he confessed that “there is no world… where [vaccine effectiveness] is the same level… we had with Delta,” and that it would take 100 days to start manufacturing a new formula at scale. A research team at Rockefeller U synthesized a spike protein early this year with 20 mutations, many the same as Omicron, and found it was “nearly completely resistant” to natural antibodies or prior vaccination. The WHO is already recommending that vaccine manufacturers start preparing new Omicron-specific formulations. Moderna is testing 3 approaches: a higher-dose booster, 2 “multi-valent” boosters designed to anticipate mutations like Omicron’s, and an Omicron-specific booster. For the time being, COVID19 booster shots may help overcome reduced efficacy with increased quantity: “defenses, if they drop, should fall stepwise, not all at once.”
“There is no world, I think, where [vaccine effectiveness against Omicron] is the same level… It’s going to be a material drop. I just don’t know how much because we need to wait for the data. But all the scientists I’ve talked to… are like ‘this is not going to be good.’” – Stéphane Bancel, Moderna CEO
So, based on what we know now, what can we say about the months ahead? In keeping with the “curve ball” metaphor…
The Game has Changed
With a vastly more contagious strain of COVID19 spreading rapidly, and infecting vaxxed and unvaxxed alike, the game has clearly changed. Those of us who are fully-vaxxed can’t expect the virus to be completely eradicated, or even to escape infection ourselves, but we can hope that our symptoms will be mild or nonexistent. For the elderly, immune-compromised, partially-vaxxed or unvaxxed, the risk is even greater, unless Omicron is substantially less virulent. At-risk individuals can no longer count on protection from the immunized majority, and venturing into public could become substantially more dangerous any day now. PHOs are advising us to exercise more caution about travel and holiday get-togethers this month, and at-risk students, staff and faculty may have to reconsider the dangers of returning to campus in January.
“We need to prepare for the worst, but not assume the worst.” – André Picard, Globe & Mail
“It really is best to act prudently and perhaps even overzealously in terms of our public health measures and our vaccination aggressiveness until we have a better idea of what exactly Omicron can or can’t do.” – Donald Vinh, infectious disease specialist, McGill U Health Centre
At best, we will need to wait until Christmas for data from laboratory tests and real-world epidemiology to tell us whether Omicron is going to outcompete Delta, whether it is more or less deadly than Delta, and whether vaccines lose enough efficacy against it to warrant reformulation. Unless Omicron is substantially less dangerous, it will still pose a threat to the immunocompromised and unvaxxed. And based on its evident transmissibility and capacity for reinfection and vaccine breakthrough, Omicron could still overwhelm our hospitals by sending a smaller fraction of a much larger group to the ICU. Either way, it’s safe to say that our focus should be on booster shots of existing vaccines for the next 3 months: Pfizer and Moderna can’t get an Omicron-specific formula through clinical trials and into manufacturing at scale until March at the earliest, and we know it will take several months to vaccinate our communities with it. If we all just need booster shots, we should be fully prepared for Omicron by March Break; if we need a new vaccine altogether, we won’t be truly ready until next summer.
The first cases of Omicron were identified among university students in South Africa, and campuses have proven to be proficient incubators of infectious diseases. The ACHA task force on COVID19 is naturally “concerned” by the rise of Omicron, and US colleges are preparing to pivot to more stringent campus precautions in January. (Some are urging KN95 masks, discouraging travel, increasing testing, or requiring booster shots.) The ACHA delayed its latest COVID19 guidance, but “our sense at this point is that the path to dealing with the variant will be to continue the multi-layers of mitigation,” including masking, physical distancing, vaccination and booster shots. Schools that have confidently abandoned masking and distancing protocols are unfortunately going to have to “reverse course,” which will be particularly difficult in states where governors have “handcuffed” institutions. Border closures in response to the Omicron variant have already had an immediate impact on student mobility, and the travel industry reports the “fear factor” has returned overnight. But the national and international flow of staff and students, home for the holidays and back in January, could stir things up significantly for the Winter 2022 term. University Business | Washington Post | Inside Higher Ed
The Next Inning
Since 45% of humanity is still unvaxxed against COVID19, “we’re still looking at a multi-year horizon” before we stop seeing new variants arise. And the truth is, the next pandemic could be “more contagious, more lethal, or both.” We’re a long way from vaccinating 100% of the population, but even if we did, “the virus could retreat into its many animal hosts, only to re-enter the human population in a slightly different form.” Governments need to invest in pandemic preparedness, we need a global approach to ensure vaccine equity, and organizations need to design resilient processes to ensure continuity through times of future disruption. “To be able to operate at speed in the context of crisis, scenarios must be simulated and decisions rehearsed.” Sydney Morning Herald | Washington Post | World Economic Forum | The Atlantic
“Adjusting our expectations to account for unpredictability, uncontrollability and the fact that our lives may be disrupted on and off, and building that into our expectations, would be good for our mental health.” – Karestan Koenen, psychiatric epidemiology prof, Chan School of Public Health, Harvard
As we wait for definitive data to guide our decisions, CdnPSE may want to ensure it has contingency plans in place for the much-touted return to “normal” in January. We may well be capping class sizes again, encouraging WFH and hybrid course delivery, and biding our time while a 6-month vaccine cycle starts all over again…
As always, thanks for reading, and my apologies if the latest pandemic trends are depressing! If you prefer, here’s some light escapism for the most wonderful time of the year…
2021 Holiday Videos
Like every year, I’m monitoring more than 700 higher ed YouTube channels for holiday greeting videos. You can check out the 50 examples I’ve already added to my 2021 Holiday Videos playlist (and please let me know if I’ve missed yours!)
Top 20 of 2020
I’ve heard from some of you that your videos are still forthcoming, so obviously it’s premature to rank this year’s crop – but ICYMI last year, I put together a comprehensive blog listing the Top 20 Higher Ed Holiday Videos of 2020.
2019 Holiday Special
Sadly, this is another pandemic December in which I simply can’t put together an elaborate video compilation for the holidays, like I did most recently in 2019. You’ll find the 3-part series, totalling 45 minutes of the best snippets from more than 500 higher ed holiday greeting videos, atop the Eduvation YouTube channel, along with 5 years of Ten with Ken Holidays Specials (totalling 3 hours) in this playlist.
Stay safe and be well, everyone!
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