COVID-19: Fred Hutchison Researcher Thread on Omicron
(17 Dec 2021)
Trevor Bedford is a biostatistician working on viruses and vaccines at the Fred Hutchison Cancer Centre. The linked thread is a few days old but gives some strong insights on Omicron's spread in several countries: South Africa, UK, Denmark, Germany, and the US. It supports much of what I've read and feared regarding Omicron's spread, though does not speak to its severity.
The first set of graphs is a log-linear plot of growth over time. On this plot, exponential growth appears as a straight line. I'd mentioned yesterday in a comment that it's likely that many countries, the US included, effectively have two simultaneous epidemics presently: Covid-Delta and Covid-Omicron. These plots support that view, with the delta and omicron infection rates presented. Several insights:
- Omicron growth is virtually straight-line dating as far back as October. And if you look at the South Africa plot, the case numbers bend upwards, that is, measured growth is accelerating. Note that on a log plot, even only slight deviations from a straight line actually represent large changes in absolute numbers.
- It's possible to extrapolate numbers backwards to determine likely first cases at the x-intercept (where the red line crosses the bottom of the graph). This puts Omicron in the US and Germany around 10 November. The UK's severe Omicron outbreak actually seems to have begun later than the US's. If you've been taking comfort that UK experience is a future portend of what's coming to the US (as I have), you might care to revise that view, though the UK's growth rate is higher than the US's, for now. As a lower graph shows, the King County, WA, doubling time is 2.2 days, faster than the UK.
- There's been little deviation from an exponential rate across four orders of magnitude. I do expect the trend to become sigmoidal / cyclical as numbers reach into the millions. But that's not happened yet.
As the text notes, doubling times range from 2.3 days (UK) to 3.3 (Germany). This is faster than the initial COVID-19 outbreak at its highest. Case numbers increase by an order of magnitude, that is, a multiple of ten, per week.
As with all surveillance and testing data, these plots are a look backwards in time, and reflect only the observed tested cases. Depending on testing lags, we've probably got another 3-7 days of actual incidence. This means multiplying by both additional growth (an order of magnitude per week) and accounting for non-tested cases (a multiplier of perhaps 3--6). Given the nearly 5 days elapsed since the thread was posted, there are two doubling periods as well. The total multiplier then is as much as 100x for present actual incidence, another two orders of magnitude over values shown. At the lower end, perhaps 30x if growth is slower and testing more comrehensive.
(Caveat: that's my Space Alien Cat interpretation. I'm not a statistician or virologist. I'm pretty comfortable making that observation though.)
In the UK, cases are growing fastest presently in London. As of December 14 (a week ago), 72% of London cases tested were Omicron. I expect that other countries, inlcuding the US, will see a similar trend. Given the "two epidemics" model, in the US, this means:
- An extant and well-established Delta wave that's been progressing north-to-south across northerly states from Minnesota to Maine, and from a south-west path from Minnesota to New Mexico. This has been gradually progressing southwards and eastwards for the most part.
- An emerging Omicron wave beginning in urban and transport hubs. New York City seems to be the present epicenter, though looking at the New York Times's hot-spot maps, Miami, FL, has emerged as an uncharacteristically hot spot in what should be the state's winter respite. Cases may be increasing in the Houston area as well. Ithaca, NY, has seen the highest rate of infections, supplanting Wheeler County, OR. Cities such as Chicago may well be at the intersection of both waves now. Illinois had been a less-affected state among the midwestern states until this past week, but is now getting hotter, with some rise in the highly urban Chicago region, but also very high rates in more rural downstate counties. Cleveland, OH, also appears hard hit.
- Several states still have very low vaccination rates, at or below 50%, notably Idaho, Wyoming, Alabama, and Mississippi. These will likely be hit very hard.
- Even previously spared (and well-vaccinated) states and territories such as Hawaii and Puerto Rico are now reporting explosive Omicron growth.
As I noted, this thread does not address severity of Omicron.
I've been watching the reports on this closely. Early suggestions were that Omicron was less severe than earlier Covid waves. The revised information from multiple sources, including South African medical authorities, the WHO, and UK, is that this is not well supported, and that the apparent mildness of Omicron may be due to its infecting large numbers of previously-exposed or vaccinated individuals. Information continues to develop, the situation is fluid, and as evidence changes, understanding and advice will likely do so as well. I'm simply relaying what I'm reading and hearing as accurately as I can.
GET VAXXED AND GET BOOSTED IF AT ALL POSSIBLE
This is Bedford's advice in a subsequent thread.
[T]he single best action individuals (and governments) can be taking to reduce impact of the Omicron wave is to get booster dose if already vaccinated and to get vaccinated if not.
Vaccination does greatly reduce severity of Omicron. "Fully vaccinated" now means two Pfizer doses and a booster.
Oh, and holiday travel and gatherings are doing absolutely nobody any favours.
As I've noted before, I expect that the US and UK will go into hard lockdown within weeks. It should do so now. I had hoped the UK would do so before Christmas, it has not. Medical advisors are telling the PM that a 2022 lockdown will be too late. Dr. Fauci in the US has been mooting the prospect of lockdowns, though Biden to date has resisted these, though less strongly over the past few days.
The biggest concern is impacts on medical and other services. Hospitals and other facilities will be and are being overwhelmed. Non-Covid issues won't be treatable due to shortages of space, equipment, and staff. Medical and other personnel will be impacted by the disease. John Campbell, RN, PhD, has noted that as much as 10% of medical staff at UK hospitals are quarantining after exposure or infection. Similar rates can be expected across all employment sectors, exacerbating production, distribution, and services further.
I'd made a lay prediction for the August 2021 -- January 2022 period that deserves review
You'll find that here.
https://joindiaspora.com/posts/52b6aff0e8f30139ede5002590d8e506
I'll admit that the US fall experience has been less severe generally than I'd feared. Vaccination seems to be helping blunt the fall-winter wave considerably. I also anticipated a greater contribution from the 2021 Sturgis Rally (which was held) than seems to have emerged. That was limited at best.
Other than that ... I think my predictions as to where outbreaks would originate and how they'd propagate were spot on.
And I'd had this to say about possible mutations:
Likely mutations are to easier transmission, longer incubation time (Covid tends to spread amongst asymptomatic carriers before onset of symptoms), efficacy of shedding, and lower-severity symptoms. This could lead to a less harmful form becoming prevalent and out-competing more harmful or lethal variants.
I'd also noted that Dr. Fauci saw US control over Covid-19 by Spring 2022 at the earliest. Given the Omicron wave ... that seems somewhat optimistic, though its spread through the population could finally precipitate a general natural immunity. Hopefully without too many more deaths, though I strongly expect the 1 million threshold to be crossed.
Again: I am not a specialist in this area, just someone following best science and reporting as I can. You are strongly encouraged to verify all content, and please comment with any concerns or inaccuracies.
https://threadreaderapp.com/thread/1471651826554470402.html
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