I apologize for the length of this post but there is a lot to unpack.  For the last month, the COVID news has been dominated by speculation about the new Omicron variant, notwithstanding that the Delta variant was still doing almost all of the damage during December.  However, it is clear that Omicron is going to quickly reset the table on the future course of the pandemic.  What that course will be is very much an open question.

Many worry that Omicron is just the latest in a never-ending string of COVID variants bred to avoid previous immunity and that the pandemic will never end.  However, some doctors and researchers are quietly and cautiously optimistic that Omicron may be the variant that ends the epidemic phase of COVID and finally turns it into an endemic disease more like the common cold or the flu.

Before getting into the current numbers, let me begin with a caveat about the metrics we have been using to monitor COVID.  As I will discuss below, the unusual characteristics of Omicron may be rendering the metrics less reliable.  In addition, the data for December is a combination of a Delta surge, particularly in the northern part of the county, and the beginning of the Omicron wave layered in on top of Delta.  But for most of the metrics we can only guess how much of each variant is contributing to the numbers.  Then add to all that we are in a holiday season with the attendant reporting delays.

Hospitalizations

As I have shared with you, I think new hospitalizations has been the best indicator of the current level of serious COVID cases.  However, Omicron may be affecting this metric.  There have always been incidental COVID hospitalizations, i.e., individuals that went to the hospital for some other condition but discovered they had COVID because everyone admitted is tested or caught COVID while in the hospital.

I have never been able to find any hard statistics on this but most of the anecdotal information seemed to indicate that it was a relatively small percentage of the total.  However, there are multiple reports that a much higher percentage of Omicron hospitalizations are incidental.  Early reports from South Africa and London have indicated that perhaps half of COVID hospitalizations have been incidental.  This analysis by The Guardian puts them at 20-30%.¹ One TMC doctor told me that about a third of their COVID hospitalizations have been incidental and Dr. Scott Gottlieb has estimated them at 30% in this wave.

This factor could make a big difference in the math.  For example, if new hospitalizations double, say from 100 to 200, but 30% of those are incidental, then the number being admitted for COVID would only be 140, a 40% increase instead of a 100% increase.

With those caveats in mind, new daily US COVID hospitalizations bottomed out on November 5 at just over 5,000 and started steadily moving back up.  But about the middle of December they exploded higher and by the end of December the seven-day average was back over nearly 15,000, eclipsing the Delta peak in late August.

If you look at hospitalizations regionally, it appears that most of the country has passed what was probably a peak in Delta admissions and began to turn down during December.  But starting about mid-December hospitalizations began to turn back up almost everywhere in the country.  In New York and New Jersey, where Omicron first broke out in this country, admissions bottomed out on November 11 and have since increased by 500%.

Closely tracking the national data, new Texas hospitalizations hit a low of 265 on November 7 and gradually drifted higher until about two weeks ago when they moved sharply up, reaching 1,431 by December 31.  Interestingly, they have eased slightly in the last three days, but there is always a possibility that is due to holiday reporting delays.  Whether they continue down or not over the next few days will be key.

Total daily hospitalizations in Texas had settled in around 3,000 through most of the month but the wave of the new admissions drove that number to 7,460 on January 3.  The only silver lining is that ICUs and ventilated patients are not moving up as quickly as hospitalizations.   There are currently about 800 ventilated patients in Texas compared to nearly 3,000 at the height of Delta.  The number of ventilated patients has been the best predictor of fatalities.

The increases have mostly been spread out across the state on a per capita basis, but Houston and Dallas are contributing significantly more than their proportionate share.

In the Houston region, hospitalizations bottomed out on December 13 at 516 but then soared to 2,200 as of January 3, a nearly 400% increase.  ICU bed usage was up by about half that amount (159→441, 177%)) during the same period.

There is a bit of an anomaly on the ventilator data for the Houston region.  The State data shows that the number of COVID patients on ventilators has gone up by about 80%.  But the SETRAC shows that the total number of ventilated patients for all causes has been flat since the Delta wave subsided.  Not sure why there is that difference. The current levels for hospitalizations and ICUs in the Houston region were about 60% and 40% at the height of the Delta wave, respectively.

It is important to point out that even if Omicron proves to be less virulent, it is almost certainly going to put a tremendous strain on hospitals over the next several weeks, at a minimum.  There are two reasons this is inevitable.  First, large numbers of staff are testing positive for the disease.  Although virtually all have been vaccinated and the vast majority have no or minor symptoms, protocols still require that they leave work.  This is one of the major reasons the CDC recently lowered its guidance for isolation from 10 to 5 days.

Second, even if the COVID infection is incidental, the patients must still be isolated from patients who do not have COVID.  This adds a whole level of complexity to the hospitals’ management of their staffs and facilities.

Fatalities

Since early November, the CDC daily fatality data has fluctuated in the 1,000-1,200 range.  There was a brief drop at the end of November but that was likely related to reporting disruptions around Thanksgiving.

For reasons I have been unable to discern, the Johns Hopkins daily fatality data, which CNN constantly displays, has consistently been significantly higher than the CDC’s official tally.  Some media hosts and guests have claimed that 2,000 people are dying daily of COVID, which is just not the case if the CDC data is accurate.

Of course, we must always keep in mind that fatalities are the ultimate lagging indicator and that effect is exacerbated during holidays.  So, we might see an increase in fatalities after the holidays.  We also don’t know how patients who die after an incidental COVID hospitalization from another cause will be characterized.  So, it will be some time before we can definitively say how Omicron is affecting fatality rates.

Before COVID, about 8,000 people died each day during this time of the year.  If all of the current reported COVID fatalities are in addition to the normal deaths, then we are running at about 10-15% more fatalities than normal.  However, that is unlikely and since we have a slightly higher population now, the excess deaths are probably running about 5-10% higher, again assuming the CDC numbers are accurate.

After a dramatic decline, the Texas date of death analysis shows that daily fatalities leveled out in mid-November at about 50.  The number moved back up slightly but then began to move down again.  There may be some significant holiday disruptions in this data, so I would not read too much into the numbers for the last few weeks. 

Vaccines

We are pretty well stalled on the number of people that are going to be vaccinated at just over 60% of the population and just under 90% of seniors.  Both of those have only moved up a few points during December.  Toward the end of December, only 150,000 people per day were becoming fully vaccinated.  That is not going to make much of a dent in the roughly 100 million Americans who are still unvaccinated.

Texas continues to rank about midway among the states with a vaccination rate at ~57% of the total population and ~85% of seniors.

Testing Results

We have always known that the new case count was a very rough gauge of the actual number of cases.  But with the appearance of Omicron, it has become even more inaccurate because Omicron is presenting such mild symptoms in so many cases.  But it is nonetheless clear that Omicron is exploding across the country.  On January 3, the CDC reported a mind-boggling 869,000 newly reported cases.  Many researchers think the real number could be twice that.  New case data from the State and TMC have recorded a similar explosion in new cases.  Nationally the positivity rate is 17% and Texas just hit an all-time high of 32%.

Breakthroughs

The CDC’s data on breakthrough cases is pretty much worthless because their latest numbers are for late November, well before the Omicron onslaught.  But all of the anecdotal information is that breakthrough infections have skyrocketed.  I am sure anyone reading this knows of someone who was vaccinated or previously had COVID but has tested positive in the last few weeks.

Fortunately, it appears that the vaccines and previous infections are still providing reasonably good protection from severe disease.  The best informed speculation is that the antibodies induced by the vaccines or previous infections do not seem to work very well against Omicron but the T-cell response does.  Since T-cells take longer to crank up than antibodies, this could explain why Omicron breakthroughs are mild and people are generally only sick for a few days.

Conclusion

The questions on everyone’s minds are how long will the Omicron wave last and how bad will it be?

There is a fairly broad consensus that Omicron is resulting in less serious illness than previous variants.  There is a debate among researchers whether that is because the world has built up so much herd immunity from vaccines and previous infections or whether it is because Omicron is inherently less pathogenic.  It is probably some of both, but there are now multiple studies which have found that Omicron is much more efficient at replicating in the bronchi and less so in the lungs.  This characteristic would explain why it is both so much more contagious but less virulent.

Many researchers have been looking to South Africa’s experience because that is where Omicron first presented and because its health reporting is considered to be fairly good.  That data from South Africa is quite promising. It shows a massive spike in new cases, to the highest level since the epidemic began there which began in the third week of November, But it quickly peaked out about three weeks later, on December 16.  Since then, the cases have gone down as fast as they went up.  In addition to being short-lived, the Omicron wave has done little to increase fatalities so far.

London, where the Omicron wave started about a week later than South Africa, has been showing a similar pattern.  It appears that cases have peaked there and while hospitalizations have risen quiet sharply, there has been almost no increase in ventilated patients or fatalities.

The other encouraging news about Omicron is that it appears to be displacing Delta.  A South African study showed that antibodies produced by an Omicron infection produced a very strong immune response to Delta, which is likely the reason it is quickly displacing Delta.

If this is correct, then massive amounts of immunity to Delta are being created by Omicron as it sweeps through the population.  It also seems likely that the reason Omicron is so short-lived is that it is quickly spreading natural immunity which is layered on top of all the previous immunity we already have from vaccines and prior infections.

We need more data to confirm the early trends we are seeing with Omicron and, of course, COVID may yet have another variant trick up its sleeve.  But every pandemic in history has ultimately ended. All of them were ultimately defeated by our immune system. None have ever been ended because of vaccines because we have never had the technology to develop a vaccine during the epidemic phase of a disease before. To be sure, vaccines have undoubted prevented innumerable new epidemic outbreaks of many diseases, but they have never stopped one.

Based on the preliminary data, Omicron may prove what Johns Hopkins professor, Marty Makary, recently described it: “nature’s vaccine.”  It will be truly ironic if we are ultimately ridded of the COVID pandemic not by our medical technology but by nature.

That is not to denigrate our technology or our efforts to minimize the damage done and still being done by the pandemic.  I think the vaccines in particular prevented millions of premature deaths globally.

However, if Omicron does prove to be COVID’s undoing, it might be a good time for us to acknowledge some humility with respect to our ability to control pandemics and show some respect for the awesome complexity and power of nature, honed over millions of years of evolution.  

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Note 1 – A major difficulty with analyzing incidental hospitalizations is that there is no accepted definition of what constitutes an incidental admission.  For example, if a patient comes to the hospital with congestive heart failure and upon admission a COVID infection is detected, was the COVID incidental to the congestive heart failure or did it cause the congestive heart failure?