Daniel R. Howard, MD, PA

OMICRON VARIANT OF COVID-19

I am very concerned about the new Variant, called Omicron (also known as B.1.1.52), being reported in the news. Here is some information about Omicron.

Background:

B.1.1.529, now labeled Omicron, was identified in a specimen collected from a patient from South Africa on November 2nd. It was reported to the WHO on November 24th. This variant has over 50 mutations compared to the original Covid-19 viral strain, with 32 of those mutations occurring in the Spike protein, which both binds to human cells, and has antibodies (from prior infections and immunizations) bind to it. Therefore, big changes in this protein are of concern, both for potential for increased spread, and for resistance to immunity from vaccination or prior infection.

Omicron’s mutations look worrisome. The Delta variant had two mutations in the region of the Spike protein called the Receptor Binding Domain (RBD), the portion that binds to human cells, and presumbably this contributed to its higher transmissibility. Omicron has ten.
At about the same time this variant was identified, there was a tremendous increase in the number of cases of Covid-19 in South Africa. The number of cases to begin with in South Africa were relatively low, 200 or 300 new cases a day. This spiked up to 2000 – 3000 over the course of a couple of days. With a fairly low baseline, it’s hard to tell what a spike means, as it could just be some statistical noise, but it certainly is a concern. Now, at this point, it’s not know whether the increased cases are due to Omicron or not, and it will be a few more days before we find this out. We do know that many of the cases in the region surrounding Johannesburg and Pretoria are due to Omicron, which increases the level of worry about this.

How did this variant start?

No-one knows for sure. However, given both the large number of untreated HIV patients in South Africa, and the very large number of mutations, it seems likely that the Covid-19 virus replicated in an uninhibited manor in a highly immunosuppressed AIDS patient, resulted in the accumulation of such number of mutations.

Where is Omicron now?

It seems to be concentrated in South Africa in the Gauteng Province surrounding Pretoria and Johannesburg, although the full extent of the spread is not clear at present. Isolated cases have been identified in several countries now, including Belgium, Australia, Britain, Italy, the Czech Republic, Germany, and Hong Kong. Thirteen proven cases, out of a total of 61 Covid-19 positive cases, were identified on two airplanes from South Africa that arrived in the Netherlands two days ago. I’m not aware if the remaining 48 have been tested for Omicron or not. There are no reported cases in the United States right now, but there will be soon.

Why the Travel Interdictions?
Well, this started in Europe, with Britain being the first nation to halt travel from Southern Africa, followed rapidly by other countries imposing travel bans, quarantines, or both. Europe is already struggling with Covid-19, with hospitals in many nations currently overwhelmed, so the presence of another problematic variant could be catastrophic. Other countries, including the US, followed the European lead.

Basically, the travel interdictions just buy a little time to figure out whether this variant is really as worrisome as it seems, and to plan for other measures that might be needed to slow the spread.

How much do we need to worry?

We don’t know at this point. While the structure and mutations of Omicron are very concerning, and the situation in South Africa are concerning, it’s really too early to know how concerned we need to be. There have been some other variants that initially looked to be worrisome, but never spread enough to be a problem. We’ll likely know within the next two weeks. I do think it is unlikely that Omicron will be completely resistant to vaccine-mediated immunity; Vaccination will probably provide some degree of protection against severe infection and death.

What can I do to protect myself?

Get vaccinated! Even if Omicron is partially vaccine-resistant, vaccines will likely provide some degree of protection. Get the primary vaccines, and get a booster when eligible.
Continue masking in high-risk environments, such as poorly ventilated indoor spaces (and avoid such spaces whenever possible, even if masked, as masking provides inadequate protection against aerosolized transmission). Limit your exposure to unvaccinated individuals. Continue to socially distance when appropriate and feasible.

COVID-19: 1.25.2021

What’s happening in the World, the US, and Maryland:

World: 99,846,375 cases worldwide. 2,140,550 deaths.

US: 25,702,125 cases. 429,490 deaths. 3416 deaths reported overnight. Rt data shows only 8 states with Rt over 1 now, which is good news, as it indicates the infection is likely to be dying out, at present, in the United States.

MD: 341,452 known total cases since the beginning of the pandemic. 2145 overnight.
6690 total deaths, 28 overnight. This number continues to decline. 1668 currently hospitalized, which has now dropped by 200 since last week. The hospitalization peak was 1952, around 2 weeks ago. There are currently 392 patients in with Covid-19 in the ICU’s across the state, and this continues to inch down as well.
State-wide 7-day positivity rate 7.21%, which continues to trend downwards.
Rt in Maryland 0.94, which continues to slowly decrease.

All of the critical indicators in Maryland, and, indeed, in most of the nation, continue to trend the right direction.

However, we are far from out of the danger zone with Covid-19. There was a lot of news over the weekend about Variant B117 (the British variant). Boris Johnson, British Prime Minister, announced it may be 30% more lethal than standard virus. However, this is based only on very preliminary population based data, and no definite evidence that this is true. Data showed that those infected with B117 were 30% more likely to die after hospitalization. While this is concerning, there is no information about comparative age or comorbidity information, which we know has a dramatic impact on mortality. For example, if the virus disproportionality infected elderly, we would expect higher death rates. There is some speculation that the 10X higher spike protein density with B117 (which almost certainly is responsible for the higher rate of spread) could cause more severe infections, but this remains speculation at this point.

What we do know about B117 is that it appears to be 50-70% more infectious, which may mean many more deaths, especially if it spreads before vaccinations are fully in place. It is now in 34 states, and is reported to be spreading rapidly in at least some of those states. It is likely responsible for an recent outbreak in an Ontario Nursing home of 130 residents, where 124 of them and most staff were rapidly infected with Covid-19, with 25 resident deaths.

I continue to be even more concerned about some of the other variants. The South African variant named 501Y.v2, is one of the most worrisome to me at the moment. There is a lot of bad news out of South Africa right now. The Eastern Cape of South Africa which was hit fairly hard in the first waves, is experiencing another terrible surge in cases. Even more concerning are the numerous anecdotal reports of repeat infections; there have been some isolated reports of this everywhere, but it seems much more common in South Africa. This is very, very worrisome to me, as it may indicate that immunity against one strain does not mean immunity to other strains. There are some in vitro (lab only) tests that this may be true, as “neutralizing antibodies” don’t seem to necessarily block the ability of the new variant to attach to human cells, although more research is needed regarding this. This variant has not yet been found in the US, but it is likely only a matter of time.

The CAL.20c variant, identified in Southern California, appears to have some of the same characteristics as the South African variant. There is less data regarding this so far, although it is now apparently widespread in Southern California.

A Brazilian variant, called P1, has infected currently 42% of patients in the city of Manaus, which is experiencing a terrible surge of infections, with hospitals totally overwhelmed and patients dying at home because there is no-one available to take them to a hospital. There was no P1 detected in November 2020 viral samples from that city. P1 carries mutations similar to both the UK and South African variants. As is the case in South Africa’s Eastern Cape, Manaus was hit devastatingly hard during the first wave in March. An article published in the journal “Science” projected that 76% of the 2.2 million residents of Manaus were infected in March. If that is accurate, it is seems likely that re-infections may be occurring, as this wave is worse than the first one. Also, with that large of a percent were really infected in the first wave, Manaus would have been well above the numbers expected for herd immunity, although that number too is increased with a more infectious version of the virus).

The Federal Government is obviously very concerned about the new variants, as the CDC abruptly restricted travel from South Africa on Saturday. In addition, President Biden has reimposed an entry ban on travelers from Brazil, the UK, Ireland, and the 26 European countries that allow relatively unrestricted travel across borders, with some tightening of the waivers available to bypass such restrictions, although that was likely planned prior to current information about the new variants.

If indeed one or more of the new variant viruses is less susceptible to protection by the vaccine, we may well be in for a real tsunami of new infection, as Manaus, Brazil, has just experienced. If you’ve ever seen a video of a tsunami, initially the sea slowly ebbs out (as we seem to be seeing with Covid in the United States right now), only to then follow with a wall of water of devastating proportions.

I truly hope this doesn’t occur. But we need to be prepared for it, for our own safety, and that of our families and friends. Getting vaccinated now (which may provide partial, if not full, protection against the new variants), practicing social distancing, masking, hand hygiene, and avoiding enclosed and poorly-ventilated interior spaces, is perhaps even more important now than at any other time in the pandemic.

COVID-19

What is going on in the world:

World: 82,519,946 cases worldwide. 1,800,813 deaths
US: 19,982,610 cases. 346,654 deaths.

General
Vaccinations Well over 2 million vaccines administered with few bad reactions As noted in clinical trials, there seems to be more side effects in those under age 55, less over 55.

Variant Covid-19.
Officially called the 2020 Kent variant, or B.1.1.7. This has noW been detected in the Colorado in a 20 year old man with no travel history, amd with no known travel contacts This means that he contracted it via community spread, so it is highly likely to be spreading throughout the US, and that is bad news.

A lookback at genomic sequences reveals that the B.1.1.7 variant was present in Brazil in April, so it is probably really not a United Kingdom source variant, as was previously suspected.

There is also now information that the South Africa variant has different set of mutations that result in the same amino acid substitution on the spike protein, so this is not due to spread from England, but an independent mutation resulting in the same spike protein change.

This is a selection advantage for this type of variant, in other words, we are seeing Darwinian natural selection in action. This is occurring due to high amount of viral replication in the world, with more opportunities for “mistakes” in the virus, some of which result in changes in the virus, some of which a beneficial for the virus (but not for its victims).

There is no indication that this variant is more deadly, but it certainly does spread more quickly. There is no reason to think that the vaccine will not work for this variant of the virus.

Data from Switzerland and the Czech republic reveal a two-fold faster spread of Covid-19 in recent weeks in those countries, believed to be due to the prevalence of the B.1.1.7 variant in those countries. That makes it even more critical to rapidly get as many people vaccinated as soon as possible!