It’s been a little while since I’ve done a COVID-19 update. Here in New York I am hoping that we are close to the peak. I’ve seen some estimates that the peak may hit this week or next. Cases continue to rise at an alarming rate. I would say based on what we’re seeing locally, the Omicron variant is behaving similarly to how it did in South Africa in that while it is extremely contagious, it also tends to produce milder disease than prior variants. Again, it’s hard to say whether that is an intrinsic characteristic of the Omicron variant or whether immunity from vaccination and prior infection plays a role. My sense based on the science so far is that it’s probably both.

As far as bench research goes, an early study out of Hong Kong showed that compared to Delta, the Omicron variant replicates about 70 times faster in the human airway (trachea and bronchi, which are tubes that carry air into and out of the lung tissue) and about 10 times slower in the actual lung tissue where oxygen and carbon dioxide exchange takes place. This is consistent with its clinical behavior, in that a ton of virus is generated in the airway where it has a chance to get out into the world and infect other people, while the amount of lung damage, i.e. pneumonia seems to be less. Another really interesting study out of Glasgow found that Omicron enters cells through endosomal fusion rather than TMPRSS2. The TMPRSS2 receptor is largely found in lung tissue, so this gives us a mechanism for why Omicron, unlike prior variants, has less affinity for lung tissue. A previous 3D supercomputer model that the NY Times reported on showed that the spike protein in Omicron is more negatively charged, so that when it floats through the air in an aerosol breathed out by an infected person, it is able to wrap lipids (fats) around itself like a blanket, protecting it from damage and potentially allowing it to linger in the air longer than prior variants.

The hospital situation is mixed. There are an almost overwhelming number of people going to the emergency room, and about half of them are testing positive for COVID-19. However, many of these people have mild symptoms and are being sent home rather than admitted to the hospital. The problem is that so many people are coming that even the small percentage that are being admitted to the hospital is causing a shortage of beds. The shortage is exacerbated by the fact that a large number of hospital staff are being infected with COVID-19 and put on quarantine. The symptoms tend to be mild because of the vaccine mandate, but it was previously a 10 day quarantine and even with the reduction to 5 days, there’s still a lot of staffing shortages. This is producing more exhaustion and burnout amongst the remaining staff who have to work more. I’ve certainly seen a lot of people who went out on quarantine and are now back, still tired from their illness but working extremely hard. Patients are starting to get admitted at a faster rate than they are being discharged, so the overall number of COVID-19 patients is building up quickly and putting a lot of stress on the whole system. Amazingly, ICU admissions have managed to stay relatively flat so far in my area with very few patients. The admissions to the ICU are about equal to the discharges. Keep in mind that an ICU discharge may mean a trip to the regular hospital unit or it may mean death. The deaths so far have occurred mostly in unvaccinated people, especially ones with other serious health problems.

I think there’s a lot of confusion about what this all means in terms of vaccines. I would say that more immunity means more protection, but there is definitely a lot of breakthrough infection with this variant. However, the breakthrough infections tend to be mild and generally do not require hospitalization unless the patient has other severe underlying medical issues. I’ve seen a number of patients with severe underlying medical issues testing positive for COVID-19 and having mild or no symptoms. The number of hospitalized COVID-19 patients who are unvaccinated is about 80-90% of the total, but the numbers are skewed because many of the vaccinated patients are being admitted for other reasons and have mild or no symptoms.

The thing about the immune system is that it has two layers. The first layer is antibodies which are easy to test against new variants and protect from any infection. The effectiveness of antibodies to the Omicron variant is greatly reduced for “full” two dose vaccination and improved, but not perfect, with a booster. The second layer is T cell immunity, which kicks in later and is less specific for a particular variant. It is also harder to measure. So while T cells may not prevent an infection, but they will fight off the infection and prevent people from becoming seriously ill. A South African study managed to measure T cell response to Omicron and it turns out that it is actually pretty darned good. So this is probably why vaccinated people are getting infections, but almost all mild ones.

Overall the hospital situation is very different from March 2020. At that time, everyone around here was terrified of going to the hospital and only the extremely ill were coming in. We had very few tests at that point and no one was willing even to leave their house to get tested. In fact, there are many stories from paramedics and EMTs of people refusing to be brought to the hospital and being found dead at home later. This refusal and fear of going to the hospital probably helped somewhat keep the hospitals from being even more completely overrun but at the same time a lot of people just died or were severely ill at home and not counted in the data. There isn’t that fear now and people are seeking medical care and testing for mild symptoms and continuing to get medical care for other issues such as heart attacks and so on. So in March 2020 what they recorded was really just the tip of the iceberg, while now we are seeing a lot more of the overall infections in the population including mild or asymptomatic cases. We can only wonder what the numbers would have looked like if we had done the amount of testing then that we are doing now.

I’ll try to end on a hopeful note. I previously wrote about having to do a medical procedure on a patient with COVID-19 pneumonia and a severe preexisting medical condition. He had been fully vaccinated, but not boosted, with Moderna. I was very pessimistic about his survival at the time but I was surprised to see that he has recovered and is now out of the ICU. I have no doubt that if he had not had a vaccination he would have died. So things are better than before. The Omicron wave passed almost as quickly as it came in South Africa. I hope things will be better here before long. Until then, you’ll want to be vaccinated and boosted and to wear an N95!