21 ms·

Omicron variant was 73% of U.S. covid cases last week

292 points by jefftk 5y ago

rblatz 5y ago
So at this point what percent of people testing positive are actually tracked? It’s still a giant pain to get a covid test and requires at least one day lead time to get scheduled in at the pharmacy. It’s so much easier to pop in to that same pharmacy and get a rapid test for $10 and do it at home.
coryfklein 5y ago
Since I don't see anyone else mentioning it here, I thought I'd call out Zvi. With all the constant noise around covid coverage, it's been such a huge relief that Zvi has been able to provide the excellent summaries that he does at least once a week. It's nearly impossible for every individual to spend enough time to parse through the deluge of information and parse the signal from the noise.
tibbar 5y ago
This is with the "Nowcast" projections on. You can disable them in the page, and this shows a measured 0.7% of cases (less than one percent) as Omicron. That's some aggressive projection model...
- Mountain_Skies 5y ago
  Probably no worse than the Imperial College London model that was used at the beginning of the pandemic to seed the response path we're all on.
  - deleted 5y ago
    [deleted]
  - ipspam 5y ago
- hn_throwaway_99 5y ago
  Agreed, I think it's important to highlight that the 73% is a projection. That said, to be clear, the 0.7% is what was measured the week of 12/4, not more recently.
  - ehsankia 5y ago
    Is there a place where we can see the raw count of samples that were sequenced in the last week and what % of them were Omicron vs Delta?
    - sndean 5y ago
      Just sticking to places with it in a simple format, there's S gene target failure rates for San Diego [0] and University of Washington [1]. I don't know if Kristian Andersen's lab has that info anywhere else, but UW has it online somewhere else, just can't reach it on my phone. It looks like both Scripps and UW are listing SGTF rates at >70% now, as of yesterday. Given that San Diego and certain counties within Washington are >70% omicron, the CDC nowcast listing it as 73% (for the nation?) doesn't seem crazy as an average. Edit: I just noticed you asked for sequencing info, but SGTF seems to be a good enough measure. Sequencing is slow, so you'll always be ~1 week out. Andersen's data is particularly good IMHO because they list Ct values <=30 and >30. It's been a pet peeve of mine for some time that certain labs run the PCR tests to Ct >40, since that could be positive with ~1 RNA molecule meaning it's unlikely that's a real infection (at least at the time of the test). [0] https://github.com/andersen-lab/SARS-CoV-2_SGTF_San-Diego https://github.com/andersen-lab/SARS-CoV-2_SGTF_San-Diego [1] https://github.com/proychou/sgtf https://github.com/proychou/sgtf
      - selimthegrim 5y ago
        There's another Omicron strain that evades the S gene failure litmus test
    - r721 5y ago
      https://covariants.org/per-country https://covariants.org/per-country ("The raw data behind these charts comes from GISAID")
- deleted 5y ago
  [deleted]
- throw8932894 5y ago
  CDC should remove note about Newcast from website. It gives wrong impression and may confuse people.
- ISL 5y ago
  If you disable "Nowcast", you go two weeks backward in time. The CDC is doing its very best to give you information here. I've been making Covid-projections since ~May using these data. This is the first time I've seen them emerge on a day other than Tuesday in months -- they got this one to market because it matters. It is my ongoing impression that the people behind these projections are doing the very best they can with the very best data available in the US. If you compare last-week's data in today's release with those released last week, you'll see a substantial refinement as new sequencing data roll in. If you're forecasting covid-trends in the US, this is one of the very best resources you've got. (Also, shout-out to the UK HSA. When the next variant comes, I hope we've gotten our latency and reporting up to your daily Omicron-report and weekly Technical Briefing level. Y'all are helping the whole world, too.)
  - dragontamer 5y ago
    > If you compare last-week's data in today's release with those released last week, you'll see a substantial refinement as new sequencing data roll in. They're doing their best, but these "Nowcast" numbers are horribly unreliable. Fortunately, that's not a big deal but hear my whole post out... Last week, two weeks ago was Nowcast as 2.something%. Now the revised numbers is like 11% for two weeks ago. To be fair: the error bars were like 0.1% to 16% on that estimate (so they "weren't wrong"... but with error bars this huge, there's no point trying to get into the nitty gritty). But even today, we can see the "73% Nowcast estimate" as an error bar of 35% to 95%. --------- The error bars are huge, but given the rate at which Omicron outcompetes Delta, we know that Omicron is doubling in roughly every 3 days. With an estimate of 30% (smallest case scenario for Omicron), we'll be at 99.9% by next week. It doesn't matter if we're at 30% today or 95% today. 99.9% Omicron is certain in the near future. We don't know if we're at 30% now or 95% now. But the era of Omicron dominance is among us right now, or maybe even a few days ago. That's incredibly important news, we may not know the exact time or day, but this is the best advanced warning we're gonna get. Omicron is here. Hopefully we all know what the new rules are by now...
    - ISL 5y ago
      Agreed on all points. The SGTF sampling by UW, Yale, and others have been more than sufficient to get a good-enough estimation, in combination with the really excellent work from the UK and Denmark, of what we're facing. Our trajectory for the next ~10+ days is largely locked-in, but strident (and empathetic) leadership may help to blunt the impact in the weeks that follow. It might be Christmas week, but if you limit contacts for the next week or two, you'll put yourself in a much-better place to be able to manage the month to come . May this be the last time humans have to pay so dearly to learn the lesson that exponentially-scaling adversaries are best-confronted when they are small.
- asdfasgasdgasdg 5y ago
  95% CI includes 35%-95% . . . with intervals that wide, the statistic seems to be questionably useful.
  - kristjansson 5y ago
    For a variant that represented 0.0% percent of cases a few weeks ago, that CI is pretty astounding.
    - asdfasgasdgasdg 5y ago
      Sure but, like, we knew this was going to happen either this week or next week, right? It was only a question of when. You know the most interesting thing about this to me is how the absolute number of delta infections decreases so much when omicron comes on the scene. This kinda implies that for at least a significant fraction of the infected, they were exposed to both delta and omicron, and omicron won. I'm really curious how that works. Does anyone know of a clear explanation of the mechanism behind that?
walterbell 5y ago
785 Omicron cases in Denmark, Dec 16 report for Nov 22 to Dec 7, Table 2, https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.50.2101146 https://www.eurosurveillance.org/content/10.2807/1560-7917.E... 0% fatal, 0.13% ICU, 1.2% hospital 4.3% Covid-recovered 76% double vax, 7% booster 14% unvax, 2% single vax 77% no travel history Edit: https://www.cnn.com/2021/12/18/politics/white-house-omicron-warning-joe-biden/index.html https://www.cnn.com/2021/12/18/politics/white-house-omicron-... > Some of Biden's advisers are encouraging the administration to begin discussing publicly how to live alongside a virus that shows no signs of disappearing ... Steering public attention away from the total number of infections and toward serious cases only -- as some Biden advisers have encouraged -- could prove a challenge after nearly two years of intense focus on the pandemic's every up and down. Edit2: https://news.ycombinator.com/item?id=29633899 https://news.ycombinator.com/item?id=29633899 > The CDC’s Nowcast algorithm has some kind of bug, and the prevalence of Omicron nationwide wasn’t really 73% in the week ending December 18. Take that to the bank ... You will see this walked back. The CDC will explain what happened. The Twitter experts will have to walk back their initial tweets. The press will have to publish a new round of articles clarifying their prior wave of headlines. It might happen tomorrow, later this week, or some time next week, but it will happen. This result won’t stand.
- dataflow 5y ago
  Update: https://www.axios.com/cdc-slashes-estimate-omicron-proportion-covid-849bc52e-259f-4f4b-9fd4-83e5008412ca.html https://www.axios.com/cdc-slashes-estimate-omicron-proportio...
- make_it_sure 5y ago
  14 deaths in UK so far, ICU and deaths are a lagging indicator.
  - thehappypm 5y ago
    14 total is very low, the UK was averaging over 100 deaths per day in October.
  - walterbell 5y ago
tapland 5y ago
The news articles stating this number are refering to data for the week ending the 11th. I can't get that data through the link, only the week ending the 4th of December with a low estimate. iOS, Sweden. Anyone else having that issue?
whatanorigtht 5y ago
jfim 5y ago
Those are some really wide 95% confidence intervals. As it is right now: Delta 26.6%, 95% CI: 5.1%-65.8% Omicron 73.2%, 95% CI: 34.0%-94.9% Others 0.1%, 95% CI: 0.0-0.4% That's not to say that Omicron isn't the majority of COVID cases (it probably is), but compared with previous weeks the intervals are really huge.
- dragontamer 5y ago
  Not really. Last week, the error bars were 0.1% to 16%, which was much more uncertainty IMO. This Nowcast model is "only" a 3x fold from lowest to highest. Sooooo... this is actually a lot more accurate and certain than last week's prediction.
  - ianai 5y ago
    Right, that’s pretty much how a 7 day in the future prediction is going to look when rates can double daily. The pattern fits from SA data roughly though. But that’s not ceterus paribus, etc.
  - jfim 5y ago
    It really depends on the question. My observation was from the standpoint of "is omicron the most prevalent variant," which this week's data suggests probably, but it could go either way. Last week's error bars would suggest that the answer to that question would be "very unlikely." As you point out, a 95% CI of 0.1% to 16% is also huge.
    - dragontamer 5y ago
      A 1% Omicron would suggest we have 6 doubling-periods before dominance, roughly 18 days. A 10% Omicron would suggest we only have 3-doubling periods before dominance, roughly 9 days (seems to be doubling every 3 days on the average). -------- The 30% vs 70% dominance question is "is Omicron going to be dominant on Thursday, or was it Dominant yesterday?". Which... isn't really that big of a difference anymore. We're just solidly in the era of Omicron now.
- 5y ago
walrus01 5y ago
google "new york coronavirus" and look at the massive past 10 day spike in the new cases chart. This isn't going to end well.
- walterbell 5y ago
  New case count arrivals should be normalized against sampling rate, there's been a massive increase in NYC test collection capacity via mobile vans and testing tents on sidewalks.
  - dragontamer 5y ago
    Sampling rate needs to be normalized against percent-positivity. NYC has gone from 3% positive to 8% positive, suggesting that NYC is missing half of its results compared to before. Remember: the flu is among us. A lot of these tests should be returning negative because the flu is spreading like normal.
  - giarc 5y ago
    https://www1.nyc.gov/site/doh/covid/covid-19-data.page#testing https://www1.nyc.gov/site/doh/covid/covid-19-data.page#testi... Positivity rate reaching 8%. 3 day lag.
  - parkingrift 5y ago
    Anecdotal, obviously, but I haven’t seen any new testing sites in Manhattan. The vans and tents have been there for months. The only change I’ve noticed is the lines. I walk past two tent sites on my way to the gym every single day. Been there for months now. I’ve never seen any significant queue until this week.
    - walterbell 5y ago
      There have been vans and big tents (10x10' approx) for months, in stable locations. More of the little booths (4x4' approx) appeared in recent weeks, in additional locations.
kesor 5y ago
Wait ... how come when you turn the "Nowcast prediction model" into OFF then there are zero Omicron cases in the US?
- renewiltord 5y ago
  Check the dates.
mostertoaster 5y ago
gargarplex 5y ago
I am mostly concerned about the mutations coming out of the Omicron contagion than the Omicron variant itself.
- UncleOxidant 5y ago
  A valid concern. Omicron is apparently mutating faster than previous variants - less genomically stable. https://twitter.com/_b_meyer/status/1470124417749557248?s=20 https://twitter.com/_b_meyer/status/1470124417749557248?s=20
  - machinelearning 5y ago
    Source?
    - UncleOxidant 5y ago
      https://twitter.com/_b_meyer/status/1470124417749557248?s=20 https://twitter.com/_b_meyer/status/1470124417749557248?s=20
  - stjohnswarts 5y ago
    Do you have a source? I follow covid news stuff pretty closely and saw nothing like that.
bruce511 5y ago
I am not a doctor, but the numbers for this varient seem encouraging. Because hospitalizations, and deaths, trend later than infections, definitive conclusions are still some weeks away. However all the data coming out of South Africa is encouraging. First, South Africa has about 25% vaccination coverage. With coverage skewing older. Infections are up [1],but hospitalizations are flat, and so are deaths. It's likely that the infection rate is grossly under-reported, especially among those without symptoms, as tests are (relatively) expensive. Annecdodally reasonably high percentages of asymptomatic infection is being detected in people being "randomly" tested (eg tested for travel and other-hospital reasons) It is also crowding out delta, which is still present, but decreasing. All in all travel bans may have been counter-productive (as well as ineffective) allowing time for more delta infections, and ultimately more deaths to take place. It's still too early to be definitive, but this may indeed be the varient we all need - one which is super contagious, but also super weak, priming immune systems against earlier varient. IF (and its a very big IF) this varient is non-fatal, then the faster and wider it spreads the better. We need to super-nova this thing, not a red dwarf. [1] https://graphics.reuters.com/world-coronavirus-tracker-and-maps/countries-and-territories/south-africa/ https://graphics.reuters.com/world-coronavirus-tracker-and-m...
- amildie 5y ago
  Encouraging why? A month from now a new vaccine-escaping variant could emerge from some squirrel in Haiti that's a billion times more transmissible than Omicron and a thousand times more lethal than Delta. The fact that this particular variant isn't an absolute catastrophe doesn't mean that a new devastating variant isn't around the corner.
  - deleted 5y ago
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  - wussboy 5y ago
    But that has never not been true in every time and in every place. Why get existential dread about it now?
deleted 5y ago
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streetcat1 5y ago
The main question is not the death or even hospitalization, but rather if you get long covid.
- zapataband1 5y ago
  Yeah most people are not talking about the long term effects of having your body fight covid... oh well, rich people can't get richer if we slow down the economy.
  - lghh 5y ago
    Actually, if we "slow down the economy" it would likely adversely affect the lower income bracket blue collar workers and other wage earners who have to be at work in person, but no longer can. I suspect most HN-goers (on average very well off) can just work from home.
  - droidist2 5y ago
    We slowed down the economy in 2020 and the rich only got richer faster.
  - icelancer 5y ago
    Amazon isn't hurting because of shutting down businesses. Small business owners are dying in droves. Slowing down the economy just means centralizing purchases to large corporations.
- giarc 5y ago
  Agree, as a young, healthy person with access to top level care (Canada) I'm not really worried about death or long hospitalization, I'm worried about long COVID. I've heard many stories of people losing taste/smell for a long time and when it does come back their senses are all messed up and what used to taste great now tastes terrible. Also stories of people that were active prior and can no longer do any exercise. I have a coworker who is a bit older, but has been off work for a few months with long COVID symptoms. That's all my real concern.
  - 5y ago
jsiaajdsdaa 5y ago
deleted 5y ago
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andrew_ 5y ago
Counterpoint: https://theprepared.com/blog/73-of-covid-cases-arent-omicron-yet/ https://theprepared.com/blog/73-of-covid-cases-arent-omicron...
- deleted 5y ago
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- littlestymaar 5y ago
  In this post there's a good point about this figure being a projection and not a measurement, but we do have actual measurements that do not require full sequencing of the virus to recognize omicron but just a PCR test. From [1]: > To gain insight into the spread of the Omicron variant in our community, we are working with a large number of partners to track S-gene target failures (SGTFs). SGTFs are a feature of the TaqPath PCR assay that fails to detect the spike gene of certain variants of interest due to a deletion in these viruses' spike gene. Most Omicron sequences have this deletion while most Delta sequences do not. As a result, the proportion of SGTF in positive tests can be used to estimate the prevalence of Omicron. Worse, the key part of the reasoning is problematic: (emphasis mine) > Assuming, as data has indicated, that Delta cases stayed approximately constant during this time, these numbers correspond to Omicron case numbers growing approximately twenty fold in one week, a doubling time of approximately thirty six hours, sustained over a two week period. > This is out of touch with what we know about Omicron. Responsible estimates of the growth rates of Omicron in populations with better data (like the UK and Denmark) and prior data on the USA, have suggested doubling times in the range of TWO TO FOUR DAYS. This has caused us (and the real experts) to characterize its rate of growth as “explosive,” and to say in late November and early December that it might attain dominance in the USA in a matter of weeks. And that’s all true. But a doubling time of 36 hours, sustained for over two weeks, is out of step with all the other data. It’s not credible. Even if 36 hours is a bit lower than most (but not all) measurement, it's not that far of the reality, while the “2 to 4 days” discussed in the article is too optimistic. A few example of doubling times: San Diego: 1.4 days [1], in the different regions of the UK, the doubling time varies from 1.5 to 2.2 days (median: 1.6 days) [2]. In France, the estimated doubling time varies from 1.6 to 2.2 days. Excerpt from [2]: > We are observing doubling time central estimates of less than 2 days for every region except the South West. This may be related to poor PCR gene target reporting coverage in this region. Oh, and in this sentence, just click on his link (which now includes data from yesterday and completely defeats his argument) > And this points to another big problem. These numbers don’t comport with the national case numbers and what we know about how variants interact[link to 3]. While huge case surges have been seen in the states in Region 2, which was already 2.4% Omicron in the latest measurements (the week ending December 4), as well as other Omicron-dominant areas like the UK, they haven’t been seen in most states elsewhere in the country. This pattern was also seen as Delta took over from Alpha in the USA this summer, but we’re not seeing it in most of the USA now. [1]: https://searchcovid.info/dashboards/omicron-estimates/ https://searchcovid.info/dashboards/omicron-estimates/ [2]: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1041833/20211216_OS_Daily_Omicron_Overview.pdf https://assets.publishing.service.gov.uk/government/uploads/... page 6. [3]: https://www.google.com/search?q=us+covid+cases https://www.google.com/search?q=us+covid+cases
NicoJuicy 5y ago
A lot of speculation. Is there a way to know the average hospital duration in SA for people without a previous infection? I know the current data in SA says it went from 8,5 days to 2,5 days. The variable currently, if the data can be cross-referenced to other countries, is the high infection rate of delta in SA. Excluding previously infected from hospital stay would create an educated guess in my eyes. If it stays <3,5 days for example, that would seem like good news.
theHIDninja 5y ago
nobrains 5y ago
These are projections. Click on "Nowcast Off" and it will only show actuals, which is a completely different picture (very little Omicron percentage).
ravel-bar-foo 5y ago
Korea is already seeing a significant uptick (doubling week on week) in imported Covid cases, mostly from the US.
mcgin 5y ago
London is right after South Africa at the vanguard of Omicron. It seems it's hospitalisation rates are only now starting to emerge. https://i.redd.it/92wwp9jp8q681.png https://i.redd.it/92wwp9jp8q681.png
- HatchedLake721 5y ago
  Have you got a link to Reddit source of the image?
  - mcgin 5y ago
    https://www.reddit.com/r/CoronavirusUK/comments/rkrjwv/londons_cases_and_hospital_admissions_20th/.compact https://www.reddit.com/r/CoronavirusUK/comments/rkrjwv/londo...
randomsearch 5y ago
As everyone keeps posting about SA and saying omicron is relatively harmless, here’s the only scientific study I’ve found on the topic, in the BMJ: “After adjusting for vaccination status, the risk of hospital admission for newly diagnosed adults is 29% lower than in the first wave,” https://www.bmj.com/content/375/bmj.n3104 https://www.bmj.com/content/375/bmj.n3104 With a doubling time of two days, this reduction in the probability of hospitalisation seems irrelevant in preventing the overwhelming of health systems. As others have pointed out, experts on Twitter seem very very worried and I’m more inclined to go with them (and the exponential function) than with my antivaxxer friend’s posts on Facebook. Here in the U.K. it already looks to me like London’s hospitals are going to be overwhelmed; I don’t understand why everyone isn’t panicking and we’re not already in a lockdown.
- blindmute 5y ago
  Nobody cares man. Lock yourself down if you're so panicked and leave the rest of us alone.
- benjaminwootton 5y ago
  We aren’t “already in a lockdown” for reasons including (but not limited to) the multi £billion cost, the harm to mental and physical health, civil liberties, the fact that people are responding to guidance, the fact that we have more than 100 million jabs issued, the fact that the modelling has been repeatedly wrong etc. If lockdowns were a free lunch then sure, let’s have them all the time! We have not seen a long term exponential growth anywhere in the world yet. Until that happens we are hiding from the bogeyman based on modelling which has repeatedly been proven incorrect (speaking from a UK perspective).
  - edanm 5y ago
    Has the modeling been wrong? Or have all the measures you wrote about above worked and prevented the "worst case scenarios" of the models?
    - zpeti 5y ago
_djo_ 5y ago
And yet the damaging travel ban against Southern Africa remains in place, even against recommendations by key US scientists...
MaxMoney 5y ago

292 points by jefftk 5y ago

So at this point what percent of people testing positive are actually tracked? It’s still a giant pain to get a covid test and requires at least one day lead time to get scheduled in at the pharmacy. It’s so much easier to pop in to that same pharmacy and get a rapid test for $10 and do it at home.

coryfklein 5y ago

Since I don't see anyone else mentioning it here, I thought I'd call out Zvi. With all the constant noise around covid coverage, it's been such a huge relief that Zvi has been able to provide the excellent summaries that he does at least once a week. It's nearly impossible for every individual to spend enough time to parse through the deluge of information and parse the signal from the noise.

tibbar 5y ago

This is with the "Nowcast" projections on. You can disable them in the page, and this shows a measured 0.7% of cases (less than one percent) as Omicron. That's some aggressive projection model...

Mountain_Skies 5y ago
Probably no worse than the Imperial College London model that was used at the beginning of the pandemic to seed the response path we're all on.
- deleted 5y ago
  [deleted]
- ipspam 5y ago
hn_throwaway_99 5y ago
Agreed, I think it's important to highlight that the 73% is a projection. That said, to be clear, the 0.7% is what was measured the week of 12/4, not more recently.
- ehsankia 5y ago
  Is there a place where we can see the raw count of samples that were sequenced in the last week and what % of them were Omicron vs Delta?
  - sndean 5y ago
    Just sticking to places with it in a simple format, there's S gene target failure rates for San Diego [0] and University of Washington [1]. I don't know if Kristian Andersen's lab has that info anywhere else, but UW has it online somewhere else, just can't reach it on my phone. It looks like both Scripps and UW are listing SGTF rates at >70% now, as of yesterday. Given that San Diego and certain counties within Washington are >70% omicron, the CDC nowcast listing it as 73% (for the nation?) doesn't seem crazy as an average. Edit: I just noticed you asked for sequencing info, but SGTF seems to be a good enough measure. Sequencing is slow, so you'll always be ~1 week out. Andersen's data is particularly good IMHO because they list Ct values <=30 and >30. It's been a pet peeve of mine for some time that certain labs run the PCR tests to Ct >40, since that could be positive with ~1 RNA molecule meaning it's unlikely that's a real infection (at least at the time of the test). [0] https://github.com/andersen-lab/SARS-CoV-2_SGTF_San-Diego https://github.com/andersen-lab/SARS-CoV-2_SGTF_San-Diego [1] https://github.com/proychou/sgtf https://github.com/proychou/sgtf
    - selimthegrim 5y ago
      There's another Omicron strain that evades the S gene failure litmus test
  - r721 5y ago
    https://covariants.org/per-country https://covariants.org/per-country ("The raw data behind these charts comes from GISAID")
deleted 5y ago
[deleted]
throw8932894 5y ago
CDC should remove note about Newcast from website. It gives wrong impression and may confuse people.
ISL 5y ago
If you disable "Nowcast", you go two weeks backward in time. The CDC is doing its very best to give you information here. I've been making Covid-projections since ~May using these data. This is the first time I've seen them emerge on a day other than Tuesday in months -- they got this one to market because it matters. It is my ongoing impression that the people behind these projections are doing the very best they can with the very best data available in the US. If you compare last-week's data in today's release with those released last week, you'll see a substantial refinement as new sequencing data roll in. If you're forecasting covid-trends in the US, this is one of the very best resources you've got. (Also, shout-out to the UK HSA. When the next variant comes, I hope we've gotten our latency and reporting up to your daily Omicron-report and weekly Technical Briefing level. Y'all are helping the whole world, too.)
- dragontamer 5y ago
  > If you compare last-week's data in today's release with those released last week, you'll see a substantial refinement as new sequencing data roll in. They're doing their best, but these "Nowcast" numbers are horribly unreliable. Fortunately, that's not a big deal but hear my whole post out... Last week, two weeks ago was Nowcast as 2.something%. Now the revised numbers is like 11% for two weeks ago. To be fair: the error bars were like 0.1% to 16% on that estimate (so they "weren't wrong"... but with error bars this huge, there's no point trying to get into the nitty gritty). But even today, we can see the "73% Nowcast estimate" as an error bar of 35% to 95%. --------- The error bars are huge, but given the rate at which Omicron outcompetes Delta, we know that Omicron is doubling in roughly every 3 days. With an estimate of 30% (smallest case scenario for Omicron), we'll be at 99.9% by next week. It doesn't matter if we're at 30% today or 95% today. 99.9% Omicron is certain in the near future. We don't know if we're at 30% now or 95% now. But the era of Omicron dominance is among us right now, or maybe even a few days ago. That's incredibly important news, we may not know the exact time or day, but this is the best advanced warning we're gonna get. Omicron is here. Hopefully we all know what the new rules are by now...
  - ISL 5y ago
    Agreed on all points. The SGTF sampling by UW, Yale, and others have been more than sufficient to get a good-enough estimation, in combination with the really excellent work from the UK and Denmark, of what we're facing. Our trajectory for the next ~10+ days is largely locked-in, but strident (and empathetic) leadership may help to blunt the impact in the weeks that follow. It might be Christmas week, but if you limit contacts for the next week or two, you'll put yourself in a much-better place to be able to manage the month to come . May this be the last time humans have to pay so dearly to learn the lesson that exponentially-scaling adversaries are best-confronted when they are small.
asdfasgasdgasdg 5y ago
95% CI includes 35%-95% . . . with intervals that wide, the statistic seems to be questionably useful.
- kristjansson 5y ago
  For a variant that represented 0.0% percent of cases a few weeks ago, that CI is pretty astounding.
  - asdfasgasdgasdg 5y ago
    Sure but, like, we knew this was going to happen either this week or next week, right? It was only a question of when. You know the most interesting thing about this to me is how the absolute number of delta infections decreases so much when omicron comes on the scene. This kinda implies that for at least a significant fraction of the infected, they were exposed to both delta and omicron, and omicron won. I'm really curious how that works. Does anyone know of a clear explanation of the mechanism behind that?

walterbell 5y ago

785 Omicron cases in Denmark, Dec 16 report for Nov 22 to Dec 7, Table 2, https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.50.2101146 https://www.eurosurveillance.org/content/10.2807/1560-7917.E... 0% fatal, 0.13% ICU, 1.2% hospital 4.3% Covid-recovered 76% double vax, 7% booster 14% unvax, 2% single vax 77% no travel history Edit: https://www.cnn.com/2021/12/18/politics/white-house-omicron-warning-joe-biden/index.html https://www.cnn.com/2021/12/18/politics/white-house-omicron-... > Some of Biden's advisers are encouraging the administration to begin discussing publicly how to live alongside a virus that shows no signs of disappearing ... Steering public attention away from the total number of infections and toward serious cases only -- as some Biden advisers have encouraged -- could prove a challenge after nearly two years of intense focus on the pandemic's every up and down. Edit2: https://news.ycombinator.com/item?id=29633899 https://news.ycombinator.com/item?id=29633899 > The CDC’s Nowcast algorithm has some kind of bug, and the prevalence of Omicron nationwide wasn’t really 73% in the week ending December 18. Take that to the bank ... You will see this walked back. The CDC will explain what happened. The Twitter experts will have to walk back their initial tweets. The press will have to publish a new round of articles clarifying their prior wave of headlines. It might happen tomorrow, later this week, or some time next week, but it will happen. This result won’t stand.

dataflow 5y ago
Update: https://www.axios.com/cdc-slashes-estimate-omicron-proportion-covid-849bc52e-259f-4f4b-9fd4-83e5008412ca.html https://www.axios.com/cdc-slashes-estimate-omicron-proportio...
make_it_sure 5y ago
14 deaths in UK so far, ICU and deaths are a lagging indicator.
- thehappypm 5y ago
  14 total is very low, the UK was averaging over 100 deaths per day in October.
- walterbell 5y ago

tapland 5y ago

The news articles stating this number are refering to data for the week ending the 11th. I can't get that data through the link, only the week ending the 4th of December with a low estimate. iOS, Sweden. Anyone else having that issue?

whatanorigtht 5y ago

jfim 5y ago

Those are some really wide 95% confidence intervals. As it is right now: Delta 26.6%, 95% CI: 5.1%-65.8% Omicron 73.2%, 95% CI: 34.0%-94.9% Others 0.1%, 95% CI: 0.0-0.4% That's not to say that Omicron isn't the majority of COVID cases (it probably is), but compared with previous weeks the intervals are really huge.

dragontamer 5y ago
Not really. Last week, the error bars were 0.1% to 16%, which was much more uncertainty IMO. This Nowcast model is "only" a 3x fold from lowest to highest. Sooooo... this is actually a lot more accurate and certain than last week's prediction.
- ianai 5y ago
  Right, that’s pretty much how a 7 day in the future prediction is going to look when rates can double daily. The pattern fits from SA data roughly though. But that’s not ceterus paribus, etc.
- jfim 5y ago
  It really depends on the question. My observation was from the standpoint of "is omicron the most prevalent variant," which this week's data suggests probably, but it could go either way. Last week's error bars would suggest that the answer to that question would be "very unlikely." As you point out, a 95% CI of 0.1% to 16% is also huge.
  - dragontamer 5y ago
    A 1% Omicron would suggest we have 6 doubling-periods before dominance, roughly 18 days. A 10% Omicron would suggest we only have 3-doubling periods before dominance, roughly 9 days (seems to be doubling every 3 days on the average). -------- The 30% vs 70% dominance question is "is Omicron going to be dominant on Thursday, or was it Dominant yesterday?". Which... isn't really that big of a difference anymore. We're just solidly in the era of Omicron now.
5y ago

walrus01 5y ago

google "new york coronavirus" and look at the massive past 10 day spike in the new cases chart. This isn't going to end well.

walterbell 5y ago
New case count arrivals should be normalized against sampling rate, there's been a massive increase in NYC test collection capacity via mobile vans and testing tents on sidewalks.
- dragontamer 5y ago
  Sampling rate needs to be normalized against percent-positivity. NYC has gone from 3% positive to 8% positive, suggesting that NYC is missing half of its results compared to before. Remember: the flu is among us. A lot of these tests should be returning negative because the flu is spreading like normal.
- giarc 5y ago
  https://www1.nyc.gov/site/doh/covid/covid-19-data.page#testing https://www1.nyc.gov/site/doh/covid/covid-19-data.page#testi... Positivity rate reaching 8%. 3 day lag.
- parkingrift 5y ago
  Anecdotal, obviously, but I haven’t seen any new testing sites in Manhattan. The vans and tents have been there for months. The only change I’ve noticed is the lines. I walk past two tent sites on my way to the gym every single day. Been there for months now. I’ve never seen any significant queue until this week.
  - walterbell 5y ago
    There have been vans and big tents (10x10' approx) for months, in stable locations. More of the little booths (4x4' approx) appeared in recent weeks, in additional locations.

kesor 5y ago

Wait ... how come when you turn the "Nowcast prediction model" into OFF then there are zero Omicron cases in the US?

renewiltord 5y ago
Check the dates.

mostertoaster 5y ago

gargarplex 5y ago

I am mostly concerned about the mutations coming out of the Omicron contagion than the Omicron variant itself.

UncleOxidant 5y ago
A valid concern. Omicron is apparently mutating faster than previous variants - less genomically stable. https://twitter.com/_b_meyer/status/1470124417749557248?s=20 https://twitter.com/_b_meyer/status/1470124417749557248?s=20
- machinelearning 5y ago
  Source?
  - UncleOxidant 5y ago
    https://twitter.com/_b_meyer/status/1470124417749557248?s=20 https://twitter.com/_b_meyer/status/1470124417749557248?s=20
- stjohnswarts 5y ago
  Do you have a source? I follow covid news stuff pretty closely and saw nothing like that.

bruce511 5y ago

I am not a doctor, but the numbers for this varient seem encouraging. Because hospitalizations, and deaths, trend later than infections, definitive conclusions are still some weeks away. However all the data coming out of South Africa is encouraging. First, South Africa has about 25% vaccination coverage. With coverage skewing older. Infections are up [1],but hospitalizations are flat, and so are deaths. It's likely that the infection rate is grossly under-reported, especially among those without symptoms, as tests are (relatively) expensive. Annecdodally reasonably high percentages of asymptomatic infection is being detected in people being "randomly" tested (eg tested for travel and other-hospital reasons) It is also crowding out delta, which is still present, but decreasing. All in all travel bans may have been counter-productive (as well as ineffective) allowing time for more delta infections, and ultimately more deaths to take place. It's still too early to be definitive, but this may indeed be the varient we all need - one which is super contagious, but also super weak, priming immune systems against earlier varient. IF (and its a very big IF) this varient is non-fatal, then the faster and wider it spreads the better. We need to super-nova this thing, not a red dwarf. [1] https://graphics.reuters.com/world-coronavirus-tracker-and-maps/countries-and-territories/south-africa/ https://graphics.reuters.com/world-coronavirus-tracker-and-m...

amildie 5y ago
Encouraging why? A month from now a new vaccine-escaping variant could emerge from some squirrel in Haiti that's a billion times more transmissible than Omicron and a thousand times more lethal than Delta. The fact that this particular variant isn't an absolute catastrophe doesn't mean that a new devastating variant isn't around the corner.
- deleted 5y ago
  [deleted]
- wussboy 5y ago
  But that has never not been true in every time and in every place. Why get existential dread about it now?

deleted 5y ago

[deleted]

streetcat1 5y ago

The main question is not the death or even hospitalization, but rather if you get long covid.

zapataband1 5y ago
Yeah most people are not talking about the long term effects of having your body fight covid... oh well, rich people can't get richer if we slow down the economy.
- lghh 5y ago
  Actually, if we "slow down the economy" it would likely adversely affect the lower income bracket blue collar workers and other wage earners who have to be at work in person, but no longer can. I suspect most HN-goers (on average very well off) can just work from home.
- droidist2 5y ago
  We slowed down the economy in 2020 and the rich only got richer faster.
- icelancer 5y ago
  Amazon isn't hurting because of shutting down businesses. Small business owners are dying in droves. Slowing down the economy just means centralizing purchases to large corporations.
giarc 5y ago
Agree, as a young, healthy person with access to top level care (Canada) I'm not really worried about death or long hospitalization, I'm worried about long COVID. I've heard many stories of people losing taste/smell for a long time and when it does come back their senses are all messed up and what used to taste great now tastes terrible. Also stories of people that were active prior and can no longer do any exercise. I have a coworker who is a bit older, but has been off work for a few months with long COVID symptoms. That's all my real concern.
- 5y ago

jsiaajdsdaa 5y ago

deleted 5y ago

[deleted]

andrew_ 5y ago

Counterpoint: https://theprepared.com/blog/73-of-covid-cases-arent-omicron-yet/ https://theprepared.com/blog/73-of-covid-cases-arent-omicron...

deleted 5y ago
[deleted]
littlestymaar 5y ago
In this post there's a good point about this figure being a projection and not a measurement, but we do have actual measurements that do not require full sequencing of the virus to recognize omicron but just a PCR test. From [1]: > To gain insight into the spread of the Omicron variant in our community, we are working with a large number of partners to track S-gene target failures (SGTFs). SGTFs are a feature of the TaqPath PCR assay that fails to detect the spike gene of certain variants of interest due to a deletion in these viruses' spike gene. Most Omicron sequences have this deletion while most Delta sequences do not. As a result, the proportion of SGTF in positive tests can be used to estimate the prevalence of Omicron. Worse, the key part of the reasoning is problematic: (emphasis mine) > Assuming, as data has indicated, that Delta cases stayed approximately constant during this time, these numbers correspond to Omicron case numbers growing approximately twenty fold in one week, a doubling time of approximately thirty six hours, sustained over a two week period. > This is out of touch with what we know about Omicron. Responsible estimates of the growth rates of Omicron in populations with better data (like the UK and Denmark) and prior data on the USA, have suggested doubling times in the range of TWO TO FOUR DAYS. This has caused us (and the real experts) to characterize its rate of growth as “explosive,” and to say in late November and early December that it might attain dominance in the USA in a matter of weeks. And that’s all true. But a doubling time of 36 hours, sustained for over two weeks, is out of step with all the other data. It’s not credible. Even if 36 hours is a bit lower than most (but not all) measurement, it's not that far of the reality, while the “2 to 4 days” discussed in the article is too optimistic. A few example of doubling times: San Diego: 1.4 days [1], in the different regions of the UK, the doubling time varies from 1.5 to 2.2 days (median: 1.6 days) [2]. In France, the estimated doubling time varies from 1.6 to 2.2 days. Excerpt from [2]: > We are observing doubling time central estimates of less than 2 days for every region except the South West. This may be related to poor PCR gene target reporting coverage in this region. Oh, and in this sentence, just click on his link (which now includes data from yesterday and completely defeats his argument) > And this points to another big problem. These numbers don’t comport with the national case numbers and what we know about how variants interact[link to 3]. While huge case surges have been seen in the states in Region 2, which was already 2.4% Omicron in the latest measurements (the week ending December 4), as well as other Omicron-dominant areas like the UK, they haven’t been seen in most states elsewhere in the country. This pattern was also seen as Delta took over from Alpha in the USA this summer, but we’re not seeing it in most of the USA now. [1]: https://searchcovid.info/dashboards/omicron-estimates/ https://searchcovid.info/dashboards/omicron-estimates/ [2]: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1041833/20211216_OS_Daily_Omicron_Overview.pdf https://assets.publishing.service.gov.uk/government/uploads/... page 6. [3]: https://www.google.com/search?q=us+covid+cases https://www.google.com/search?q=us+covid+cases

NicoJuicy 5y ago

A lot of speculation. Is there a way to know the average hospital duration in SA for people without a previous infection? I know the current data in SA says it went from 8,5 days to 2,5 days. The variable currently, if the data can be cross-referenced to other countries, is the high infection rate of delta in SA. Excluding previously infected from hospital stay would create an educated guess in my eyes. If it stays <3,5 days for example, that would seem like good news.

theHIDninja 5y ago

nobrains 5y ago

These are projections. Click on "Nowcast Off" and it will only show actuals, which is a completely different picture (very little Omicron percentage).

ravel-bar-foo 5y ago

Korea is already seeing a significant uptick (doubling week on week) in imported Covid cases, mostly from the US.

mcgin 5y ago

London is right after South Africa at the vanguard of Omicron. It seems it's hospitalisation rates are only now starting to emerge. https://i.redd.it/92wwp9jp8q681.png https://i.redd.it/92wwp9jp8q681.png

HatchedLake721 5y ago
Have you got a link to Reddit source of the image?
- mcgin 5y ago
  https://www.reddit.com/r/CoronavirusUK/comments/rkrjwv/londons_cases_and_hospital_admissions_20th/.compact https://www.reddit.com/r/CoronavirusUK/comments/rkrjwv/londo...

randomsearch 5y ago

As everyone keeps posting about SA and saying omicron is relatively harmless, here’s the only scientific study I’ve found on the topic, in the BMJ: “After adjusting for vaccination status, the risk of hospital admission for newly diagnosed adults is 29% lower than in the first wave,” https://www.bmj.com/content/375/bmj.n3104 https://www.bmj.com/content/375/bmj.n3104 With a doubling time of two days, this reduction in the probability of hospitalisation seems irrelevant in preventing the overwhelming of health systems. As others have pointed out, experts on Twitter seem very very worried and I’m more inclined to go with them (and the exponential function) than with my antivaxxer friend’s posts on Facebook. Here in the U.K. it already looks to me like London’s hospitals are going to be overwhelmed; I don’t understand why everyone isn’t panicking and we’re not already in a lockdown.

blindmute 5y ago
Nobody cares man. Lock yourself down if you're so panicked and leave the rest of us alone.
benjaminwootton 5y ago
We aren’t “already in a lockdown” for reasons including (but not limited to) the multi £billion cost, the harm to mental and physical health, civil liberties, the fact that people are responding to guidance, the fact that we have more than 100 million jabs issued, the fact that the modelling has been repeatedly wrong etc. If lockdowns were a free lunch then sure, let’s have them all the time! We have not seen a long term exponential growth anywhere in the world yet. Until that happens we are hiding from the bogeyman based on modelling which has repeatedly been proven incorrect (speaking from a UK perspective).
- edanm 5y ago
  Has the modeling been wrong? Or have all the measures you wrote about above worked and prevented the "worst case scenarios" of the models?
  - zpeti 5y ago

_djo_ 5y ago

And yet the damaging travel ban against Southern Africa remains in place, even against recommendations by key US scientists...

MaxMoney 5y ago