Here is a summary of news and information about the COVID-19 Omicron variant, on December 1, 2021 -
- The first case of the Omicron variant in the U.S. was detected in SF
- Worldwide Omicron cases = 426 in 36 countries
- Probability of finding more cases in the U.S. is high based on travel patterns from Southern Africa
- Researchers expect some immune escape and higher transmissibility properties of Omicron
- Researchers suspect that the Omicron originated in an immunocompromised individual or perhaps in an animal
- A study from September hints at Omicron having high antibody resistance
- But researchers expect T-cell immunity and booster shots to provide protection against severe disease
- Case numbers are still increasing sharply in S. Africa
- A case in Israel may have originated in London
- Indirect way to detect Omicron hints at spreading in the UK
- It will take weeks to understand Omicron transmissibility, severity and immune evasion.
Omicron in the U.S.
The first case of the COVID-19 Omicron variant in the U.S. has been detected in San Francisco. The individual had returned from South Africa on Nov 22, 9 days ago, was fully vaccinated (does not say 2 or 3 doses) and has mild symptoms. It is not an unexpected development; it’s just surprising why it took so long to discover it.
Worldwide Omicron cases
Latest case numbers for Omicron from bnonews.com/…. That’s 426 confirmed cases in 36 countries.
Country Probabilities
The following shows the travel patterns from South Africa and Botswana to various countries, which reflect the relative probabilities of Omicron traveling to these countries, assuming the variant originated in S. Africa or Botswana. According to this analysis, we should expect more cases in the U.S. More details at www.covid-19-mobility.org/...
Evaluation and prediction about Omicron’s properties
This is a good thread trying to estimate the transmissibilty vs immune evasion properties of Omicron. We do not have enough data to narrow down the range of the parameters, but it shows how one might go about calculating it with incomplete and imprecise data and fine tune it as more data arrives. Note that a given high measured rate of spread can be caused by an increase in transmissibiity or an increase in immune escape or some combination of both. More data is needed to compute these two factors more accurately.
This is science, not the BS you see on twitter where people put out numbers with no basis, no uncertainties, no confidence intervals, no sources, just based on their hunches, saying things people want to hear.
Omicron origin
This is a long thread by a top notch Infectious diseases and genomics expert. He dissects a lot of available info coupled with fundamental principles of genomics and statistics. As is usual with real scientists, there are no definitive answers yet, only the range of realistic possibilities and probabilities. The following section is intriguing on the possible origin of this 50-mutation Omicron variant — Dr. Andersen leans towards the animal reservoir hypothesis -
Here is a good article discussing the 3 hypotheses; opinions from experts are divided over this issue, given the paucity of data at this moment.
What has scientists concerned?
It’s the high number of mutations, many of them known from previous variants to affect transmissibility and immune escape. The comparison between Delta and Omicron is concerning.
But scientists cannot precisely predict how the virus will behave with this combination of mutations. Empirical data from the field will provide definitive answers.
Another Prediction of Immune Escape
Based on a study of a lab-made variant against two doses of an mRNA vaccine, Prof. Paul Bieniasz expects Omicron to be highly antibody resistant. But he is optimistic that booster shots and/or prior infection will provide protection.
Also, we will hear in coming days of protection by T-cell response, which is generated by vaccines, esp. with a booster. A variant like Omicron will have difficulty evading T-cell response.
Gauteng province, SA
Case growth in Gauteng province, SA has scientists concerned. It is mainly Omicron cases in this province. 3-day doubling rate is quite high, that too in a province with a high level of immunity due to infections and vaccinations.
8,561 cases today in S. Africa, 4,373 yesterday, moving average was just 774 a week ago.
Weekly hospitalizations in Gauteng province have also seen a sharp increase. The last point in the graph covers just 4 days of the current week.
Spreading in the UK?
This data hints that Omicron may be spreading in the UK. The S gene target is detected in Delta but not with Omicron due to it mutation in COVID tests. This S gene target failure (SGTF) metric will be closely monitored by scientists around the world, since it provides an early estimate of Omicron prevalence before full sequencing data is available.
Cases in Israel
Two recent cases in Israel. An MD/PhD cardiologist, Pfizer 3 doses, returned from London on Nov 23, tested positive on Nov 27, ended up infecting a colleague. Believes he caught the virus in London. www.theguardian.com/...
The symptoms are mild. From www.cnn.com/…
The doctor's PCR tests before leaving Britain and on arrival back in Israel had produced negative results, so the man returned to work where he infected another doctor, a man in his 70s, the hospital says.
The pair are now resting at home with only very mild symptoms. All those who were in contact with the two men have been tested, with no positive results so far.
Epilogue
This U.S. case discovery is not unexpected. In fact, more Omicron cases can be expected, as cases develop and we do genomic testing. The earlier we detect them, the better our chances to contain the spread of the virus.
Note that we still do not know the properties of this variant — transmissibility, severity and immune evasion, so this case is not cause for alarm.
Note that this diary presents data and opinion from respected experts; I am not an expert in this field and I offer no predictions, hunches or medical advice.
Meanwhile we all know the drill — stay informed and vigilant, get the booster shot, mask, social distance, and encourage others to do so. And keep fighting against the right-wing disinformation campaign.
Please check out these other diaries for more in-depth info. on Omicron —