The C.D.C. significantly lowers its estimate of Omicron's prevalence nationwide
Source: New York Times
The Centers for Disease Control and Prevention estimated that the Omicron variant now accounts for roughly 59 percent of all Covid cases in the United States, a significant decrease from the agency’s previous estimate. The update shows how hard it is to track the fast-spreading variant in real time and how poorly the agency has communicated its uncertainty, experts said. Last week, the C.D.C. said that Omicron accounted for approximately 73 percent of variants circulating in the United States in the week ending Dec. 18. But in its revision, the agency said the variant accounted for about 23 percent of cases that week.
In other words, Delta, which has dominated U.S. infections since summer, still reigned in the United States that week. That could mean that a significant number of current Covid hospitalizations were driven by infections from Delta, Dr. Scott Gottlieb, a former commissioner of the Food and Drug Administration, suggested on Twitter. Hospitalizations typically lag several weeks behind initial infections. Experts said they were not surprised by the revisions, given that the C.D.C.’s estimates are rough guesses, with a wide range of possible values known as “confidence intervals.”
Cases of Omicron can only be confirmed by genetic sequencing, which is only performed on a portion of samples across the country. And Omicron is still spreading extremely fast. Still, they said the C.D.C. did a poor job communicating the uncertainty of its estimates. “The 73 percent got a lot more attention than the confidence intervals, and I think this is one example among many where scientists are trying to project an air of confidence about what’s going to happen,” said David O’Connor, a virologist at the University of Wisconsin-Madison. Dr. O’Connor said he initially thought the initial 73 percent point estimate “seemed high.” The agency came up with the estimate based on a “relatively small number of sequences,” he added.
“It’s like playing Name That Tune, and trying to say, based on just the first note, if the song is Ice Ice Baby by Vanilla Ice, or Under Pressure,” Dr. O’Connor said. “Without more data it can be really hard to know which one it’s going to be.” The new estimate of 59 percent is also a rough calculation, experts said, and will most likely be revised in future weeks. “I just want people to be very aware that that is an estimate, that’s not actually from sequence-confirmed cases,” said Nathan Grubaugh, an epidemiologist at the Yale School of Public Health. “With Omicron in particular, it’s been very difficult to have any sort of projections, because things are changing just so so rapidly.”
Read more: https://www.nytimes.com/live/2021/12/28/world/omicron-covid-vaccine-tests/the-cdc-significantly-lowers-its-estimate-of-omicrons-prevalence-nationwide
Interesting because I had just checked for updates on their bar charts.
The one done 12/18/21 was this -
The latest is this -
I think they use models that estimate a certain infection rate based on what data they have and then extrapolate from there. However with a still-small number of actual sequencing being done, the estimates will have a higher bias towards those actually doing sequencing, thus introducing a lot of uncertainty. But as other locales start ramping their sequencing up, those places may not be seeing the surge yet.
= new reply since forum marked as read
Last edited Tue Dec 28, 2021, 05:47 PM - Edit history (1)
Philly just surpassed it's average highs. We had been averaging around 30 - 40 cases per capita and are now up to 89 -
by Erin McCarthy, Jason Laughlin, and Max Marin
Updated 27 minutes ago
The seven-day average of new coronavirus cases in Philadelphia is the highest it’s ever been as the extremely transmissible omicron variant continues to surge in the region. The city was averaging 1,407 new cases per day as of Monday, surpassing the previous record of 1,235 set on Dec. 8, 2020. The number has shot up in recent weeks, increasing fivefold since Nov. 30. “The concern’s high,” said Patrick Kelly, an intensive care unit nurse at Einstein Medical Center, which is already near capacity with sick patients. “More people are in contact with people who are positive. It’s the same thing with everyone you talk to.” As hospital surges typically lag weeks behind case surges, health officials and residents are holding their collective breath to see whether hospitals here become overwhelmed.
Clarity on how many of those recently infected will need to be hospitalized should come in mid-January, said several experts. While early research out of South Africa, England, and Denmark indicates that the omicron variant may be less likely to send people to the hospital, especially if they are vaccinated and boosted, the speed with which omicron is spreading could still overwhelm providers, even if a smaller percentage of those infected get very sick. Emergency departments are already taxed, with waits to be seen ranging from four to six hours at city hospitals. Should cases continue to rise, hospitals may need to reinstate emergency measures taken during previous surges, including canceling some non-urgent procedures and converting other wards into ICUs.
“We really don’t want to go there like before,” said Rohit Gulati, Einstein Health System’s chief medical officer. “but if it did come to that that’s what we would be forced to do.” Emergency departments are already taxed, with waits to be seen ranging from four to six hours at city hospitals. Should cases continue to rise, hospitals may need to reinstate emergency measures taken during previous surges, including canceling some non-urgent procedures and converting other wards into ICUs.
More than 39,000 Philadelphians were tested at city sites from Dec. 20 to 22, heeding the advice of health officials, including Philadelphia health commissioner Cheryl Bettigole, who urged testing before seeing family or friends for the holidays. Even more people took at-home rapid tests, which are not accounted for in official records. Distressing records are being set in the suburbs, as well, with the seven-day average of new cases per 100,000 people reaching pandemic highs in both the Pennsylvania suburbs and South Jersey. The average in South Jersey is the highest, at 110.8 cases per capita.
(snip)
https://www.inquirer.com/health/coronavirus/philadelphia-covid-cases-omicron-testing-pa-nj-20211228.html
(let alone correctly report) their data and blue states with wonky data systems that need a lot of care and feeding, where actually sequencing of the virus itself requires specific equipment, time and resources to do, then yeah, you are going to get "ballparks" based on what you have.
You then have the media and the public demanding to know what variant is circulating RIGHT NOW!!11!!!1!!!! and here we are. 
The problem was ID'd back in February -
By MJ Lee and Michael Nedelman, CNN
Updated 7:01 AM ET, Thu February 11, 2021
(snip)
The US has been ramping up its sequencing efforts and is on track to process at least 7,000 samples per week, Walensky previously said. But she has also echoed statements that more sequencing is needed to track the spread of variants across the country. A CDC official previously told CNN that the UK and some other countries have a more centralized system for doing sequencing. But in the US, several different types of labs -- federal, state, academic and private -- are doing the work.
Denmark, for example, launched an effort to sequence all positive samples starting January 12, a spokesperson for the government's public health institute told CNN last week. Before that, the institute, called Statens Serum Institut, fully sequenced about 20% of positive samples from the start of the pandemic.
Only eight states have genetically sequenced more than 1% of their total coronavirus cases during the pandemic, compared to a national average just under 0.4%, according to CDC data. Eighteen states have sequenced less than 0.1% of their confirmed cases. Experts have previously told CNN that the US should aim to sequence 5% to 10% of cases, in line with sequencing efforts in the UK. Given cases over the past seven days, this would amount to roughly 38,000 to 76,000 sequences in a week.
(snip)
https://www.cnn.com/2021/02/11/politics/biden-administration-covid-variants/index.html
Since then, there have been improvements -
By Jacqueline Howard, CNN
Updated 4:46 PM ET, Fri December 3, 2021
(snip)
Sequencing many more specimens than a year ago
Genomic sequencing involves examining and decoding the genetic material of a virus to identify how it has changed over time. These changes occur as mutations. Kelly Wroblewski, director of infectious disease at the Association of Public Health Laboratories, said in a written statement to CNN that sequencing can take just a couple days, but for many, it's longer. We generally say about a week," Wroblewski said. It's not as simple as a Covid-19 test with a swab. Only samples that are sent into laboratories for diagnostic testing can be sequenced to look for the genetic evidence to tell which variant of virus has infected someone.
The types of tests -- diagnostic and sequencing -- are done separately. Polymerase chain reaction or PCR testing makes the process easier. Quick antigen tests are not used to detect variants, nor are tests people take on their own at home. Earlier this year, in January, an international database showed the United States ranked 61st in how quickly virus samples were collected from patients, analyzed and then posted online -- taking about 85 days. Countries with far fewer resources, including Bangladesh, Sri Lanka and Suriname, processed samples more quickly than the United States.
As of November 24, based on data from the global science initiative GISAID, the United States appears to have moved up the list to rank 21st when it comes to the speed of collecting samples, sequencing and reporting results, taking a median of about 28 days. An analysis of GISAID data by the Broad Institute of MIT and Harvard also ranked the United States 21st in terms of how many sequences are performed per 1,000 Covid-19 cases, as of November 24.
"Back in January, the numbers were quite low. It was really I think under half a percent in terms of the Covid infections that were prevalent were getting sequenced," said Dr. Ingrid Katz, associate faculty director of the Harvard Global Health Institute and an associate professor at Harvard Medical School. The UK, for example, was sequencing around that time around 5%. Denmark was around 12%. Australia, they were doing like 60% of their detected viruses were getting sequenced," Katz said. "So, now we're in a better place, I would say, in turn, just because the federal government has infused more cash."
https://www.cnn.com/2021/12/03/health/coronavirus-genome-sequencing-omicron/index.html
and so have most public health organizations around the globe.
Why? Because the public only sees the headline in most announcements and rarely studies the full context. So, when the CDC or UK's NHS says "Omicron not nearly as severe", most citizens take that to mean they can be much less cautious over masking or even getting vaccinated. I noticed that headline or its equivalent dozens of times even before Omicron had been thoroughly studied.
I've seen that happen almost daily since the beginning of this pandemic. Outfits like CDC should have citizen interpreters on-staff just to evaluate all the different contexts of public statements prior to issue.
We scientists are far too naive and trusting of other's thinking and tend to speak as if we're addressing a room full of scientists and engineers, all of whom would instinctively question everything and instinctively look at things from all angles. That does not happen in the minds of our general public.
KYEG.......
Trying to get a bunch of geeks and nerds (and I say this as a retired chemist) to engage in what amounts to "pop science" that accurately reflects the situation (without the complexity and getting into the weeds), is difficult to pull off.
I know there were a bunch of OPs recommending viewing the Netflix film "Don't Look Up" (and I finally did a couple days ago) but the DiCaprio character was the personification of this and perfectly captured the difficulty that many scientists face trying to distill something complex down to what is essentially "sound bites". 
but then you have those who would then debate whether the interpretation aligned with "the King James version" or "the New Revised edition" or... or... 
