Early Warning: Omicron
“We may well end up with both Delta and Omicron circulating at the same time. Omicron preying on the vaccinated and those with strong ‘immunity’ from prior infection. Delta will prey on those whose ‘immunity’ has waned, is waning or who are unvaccinated. It’s even conceivable that we’ll be susceptible to one or the other, at different moments, as we cycle through our own particular ‘immunity spectrum.’ We should work collectively to eradicate Omicron before it’s too late.”
Updates
Imperial College London’s React study – which has been updated monthly since May 2020 and is funded by the U.K. government – analyzed 100,607 PCR test results from across England. Swabs were collected between Jan. 5 and Jan. 20.
Two-thirds of the 3,582 participants who tested positive in January reported they had already tested positive for Covid in the past. A further 7.5% of infected participants said they suspected they had previously had the virus, but had not had this confirmed with a test.
“We observed unprecedented levels of infection with SARS-CoV-2 in England in January 2022 and almost complete replacement of delta by omicron,” the study’s authors said in their paper released Wednesday.
https://twitter.com/drericding/status/1485354857339011080?s=12
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After Om v1.0, you can catch mom v2.0
“Virus researcher Anders Fomsgaard. (Anders Fomsgaard, chief physician and virus researcher at SSI) …. The high infection rates have also led to more professionals starting to talk about herd immunity…But a sub-variant of Omikron called BA.2 can now threaten group immunity, explains Anders Fomsgaard, who is chief physician and virus researcher at SSI.
– It is possible that you can be infected with BA.1 Omikron first, and then you are not immune to being infected immediately afterwards with BA.2, he says in ‘Go morgen Danmark’.
In Norway, where BA.2 is also spreading, cases have been seen where this has happened.
When the Omikron variant came to Denmark in December, BA.2 accounted for about 2 percent of infection cases, but in January it outperformed BA.1, and now accounts for more than half.
– It may also be that it is more resistant to the immunity that is in the population, which allows it to infect better. We do not know yet, says the virus researcher.
– In fact, the two are as different from each other as the Alpha variant was from Wuhan, so there are some quite marked differences when looking at immunity and infection, Anders Fomsgaard explains.
One thing he emphasizes, though.
– The vaccines still work
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This is the first time i’ve seen someone of this ilk say Omicron’s on a par with measles.
Former director of CDC.
Reading between the lines, he’s probably thinking it’s even a lot worse than measles.
Up until three weeks ago anyone saying anything could be more contagious than measles would have been laughed out of it and seen as a crank:
In all fairness, I called the above two weeks before SAGE, the UK government’s scientific advisory committee raised the possibility that instead of replacing Delta, Omicron might complement it.
Each preying on different markets:
SAGE 98 minutes: Coronavirus (COVID-19) response, 7 December 2021
Published 8 December 2021
https://www.gov.uk/government/publications/sage-98-minutes-coronavirus-covid-19-response-7-december-2021/sage-98-minutes-coronavirus-covid-19-response-7-december-2021
Omicron Overview
Two new candidates for inclusion on the W.H.O.’s list of Variants of Concern came to the attention of European scientists on Wednesday night, after a British scientist posted a précis of the molecular charateristics of one of them on Twitter.
The last significant global declared Variant of Concern was Delta last Spring.
Of the two new potential Variants of Concern B.1.1.529 appears to be the most known and indeed feared.
The other however C12 appears also significantly more contagious than Delta.
B.1.1.529 was designated as Omicron on Friday by the World Health Organisation.
South Africa’s public health officials have stated that the reproductive rate of Omicron in the province where it was first identified (but does not necessarily come from) is an astonishing 1.93.
Any number over 1 signifies exponential growth.
In the course of only a few weeks, Omicron has outcompeted Delta.
It is estimated to be 500% faster than Delta at spreading.
For comparison Delta was 70% faster than the original Variant.
If these modelled calculations hold true, then it has also been calculated that Omicron could have a R0 of around 20.
This means that on average each infectious person will infect a further 20 people.
By comparison, Delta was already more transmissible than MERS, SARS-CoV-1, Ebola, flu and small pox.
Delta was estimated to be as contagious as chicken pox.
Measles is more contagious than all of the previously mentioned viruses with an R0 of 15.
It has been shown over and over again that how fast a virus spreads is a better predictor at how many people it harms than its capacity to evade immune responses.
Omicron however appears to be able to evade vaccine-induced “immunity.”
Two genomically sequenced cases in Hong Kong had both had double doses of Pfizer.
At the time of writing there are media reports that one of four Omicron cases identified at Israel’s borders had had three doses of Pfizer.
The Hong Kong government published a case report of the two cases it had identified in one of its quarantine hotels.
Here is a summary:
“…Stayed in rooms opposite… Case 1 + with a CycleThreshold 18…Case 2 + w/ a Ct value 19… Case 2, … might have been infected with virus while air flowed to corridor when case 1 opened hotel door without wearing a mask, coupled with unsatisfactory airflow…”
[https://www.news.gov.hk/eng/2021/11/20211123/20211123_102145_582.html type=category&name=covid19&tl=t]
The number of cycles of amplification for those two cases to be identified was very low at 18 and 19.
Generally speaking, PCR samples need to be amplified 30 times before Covid’s signature is identifiable.
In these cases even though they were vaccinated and had been tested before while in quarantine such low Ct’s suggest Omicron replicates with extraordinary speed inside the body.
It is notable that Delta replicates 1000x faster than Alpha, which replicated around 18x faster than the WildWuhan Version.
WildWuhan version infectious individuals breathed out 1m+ virus particles an hour.
This speed of replication means that even if people have antibodies or T cells to fight against Omicron, Omicron will overwhelm the body before those T cells or antibodies have a chance to attack it.
Apart from these empirically derived signals that Omicron is something extraordinary even in a pandemic of extraordinary events is the molecular composition of its genome.
Omicron has many combinations of mutations previously unseen in any of the millions of sequenced Covid genomes.
One particular feature is highlighted as of great concern by experts.
Sars-CoV-2 was the first human coronavirus with what’s known as a Furin Cleavage Site on its spike protein.
This accounts for Covid’s 20x better affinity to our bodies ACE-2 receptors which are practically everywhere in our body – even, it has just been discovered on the follicles of our ear hair.
Sars-CoV-1 did not have this FCS, thus it was less contagious.
Omicron has two mutations on its spike protein’s furin cleavage site (FCS).
This could well be part of the mechanism which explains how it is so contagious.
How many Omicron virus particles breathed out per-hour is a key question as yet unanswered?
But an infectious Delta person breathes out 18 billion virus virions-per-hour.
And given that it is eight hours before a Delta infectious person’s infection can be detected by PCR tests, an average Delta infectious person will breathe out 144 Billion virions before a PCR test can detect they’re Covid positive.
First modelled calculations suggest Omicron may be 4.5x faster than Delta:
Now, there are those who argue (and maybe for good reason) that Omicron isn’t quite as transmissible as that.
However, we probably shouldn’t feel any succour from their rationale.
We may well end up with two circulating variants – Delta and Omicron- each with a different market.
Omicron preying on the well vaccinated, as well as those with strong ‘immunity’ from prior infection.
While Delta will prey on the unvaccinated, partly vaccinated and those of us whose ‘immunity’ from vaccines or prior infection has faded.
Or the other way around.
Viruses, like products or predators in any market, have an entrepreneurial spirit all of their own.
They often find previously unimagined niches.
The Jerusalem Post published preliminary data on Omicron, based on contact tracing of a doctor who arrived in Israel infected by Omicron.
Preliminary calculations found Omicron to be 1.3x as transmissible as Delta.
This would make Omicron 2.73x transmissible as the original now extinct WildWuhan version of Covid.
These preliminary data also suggest Omicron infected have a 2.4x chance of “developing serious symptoms” as those with Delta.
Delta has already infected 5 Million Britons (and 1.4m children) since July. July 2021!
It takes between one and three virions for 99% of Covid infections to establish themselves.
The Omicron variant has the capacity to transform the world’s approach to Covid, but only after a lot of suffering.
Characteristically, the countries which have so far done best to defeat previous variants – Israel, Japan, Hong Kong and elsewhere – have not taken a “wait and see” and “hope for the best” approach to dealing with Covid.
They have taken a precautionary approach.
It’s worth noting that there is not a single occasion since March 2020 when a precautionary approach hasn’t, in hindsight, been justified by how things turned out!
Countries which have immediately adopted stringent measures – such as FFP3 mask mandates, providing HEPA air cleaning technology and adjusting routines to the nature of the actual environmental security threat have fared better in terms of sustaining operations throughout the pandemic.
Given what we already know about Omicron, and it’s multiplicative potential to complement Delta, wise States and organisations should do likewise now.
