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Omicron news

In terms of possible sharpness of wave I'm not focussed on health issues exclusively either. There were various bullets we dodged in the past in terms of infrastructure and supplies due to staff sickness levels during wave peaks being high but still just within coping thresholds. I should not be complacent about whether that will remain the case in a very fast spreading wave.
 
Oops there was one more quote from those SAGE minutes that I meant to include but missed out in my previous post about that:

19. Some international reports of ‘superspreading’ events (some of which include Omicron) also suggest a greater role for airborne transmission than has previously been the case, as it is less likely that Omicron could have spread to as many people as it has at those events by other routes (low confidence). This means that measures to reduce airborne spread such as ventilation, well-fitting masks and distancing or reduced density of people in indoor environments may be even more important.
 
I've still not seen any graphs of modelling results yet LynnDoyleCooper but there is now a document about the SAGE modelling groups latest consensus statement:


I dont know which bits to quote to do it justice, so here is just a flimsy first attempt:

16. Initial preliminary modelling has been conducted by two academic groups to consider the potential implications of a variant with immune escape (from both vaccine-induced and natural immunity) and transmission advantage.

17. Any wave of significant infection, almost irrespective of immune escape, will spill over into hospitalisations, and ultimately deaths. If initial estimates of transmission advantage and immune escape from South Africa are applicable to the UK population, there is the potential for a very substantial peak of infections much larger than occurred during the winter wave of January 2021. Even if severity of omicron were half that of delta, the sheer number of infections could lead to significantly more pressures on health and care settings; currently there is no strong evidence that omicron infections are either more or less severe than delta infections.

18. If omicron’s immune escape reduces vaccine effectiveness against hospitalisation from, say, 96 per cent to 92 per cent, that would effectively double the number of vaccinated individuals who are not protected from hospitalisation.

23. Assuming that omicron has the same severity or pathogenicity as delta, all modelled scenarios from the three groups so far have qualitative similarities across sensitivities analysed, irrespective of immune escape and transmissibility assumptions made and the interplay between these. Even assuming the lower end of this observed growth rate, many scenarios see hospitalisations close to or going beyond previous peak levels, if there is no reduction in transmission. The situations where the peak of the epidemic is below 1,000 to 2,000 omicron hospital admissions per day (without intervention) require low immune escape and very high protection from boosters to be consistent with observed growth.

24. The rapid rate of increase currently observed suggests that omicron-based hospital admissions alone could be of the order of 1,000 per day by the end of 2021.

28. Given the known data issues and potential for different test-seeking behaviours around the festive period, it is possible the scale of cases and hospitalisations over this period will be very difficult to track at a critical time for the epidemic.

30. The relative severity of omicron compared to delta remains unknown. Changes in the level of hospitalisations will broadly scale linearly with changes in severity, assuming no change in hospital capacity as admissions increase, and a marked decrease in severity is unlikely to offset the impact of a larger susceptible pool and or increased transmissibility; it would be easier to halve the number of infections than the infection hospitalisation rate (IHR).

They had another meeting yesterday, since the one this document covers, and I know nothing about that one yet.
 
I am getting a little muddled about timelines.

When did we first hear about Omicron?

When did South Africa first classify it and when did they have the first surge of cases?

What was the time from infection to hospital deaths of delta?

So when can South Africa expect their first deaths, if that is the MO of Omicron?

And likewise, when can the UK expect them?
 
I am getting a little muddled about timelines.

When did we first hear about Omicron?

When did South Africa first classify it and when did they have the first surge of cases?

What was the time from infection to hospital deaths of delta?

So when can South Africa expect their first deaths, if that is the MO of Omicron?

And likewise, when can the UK expect them?

South Africa told the WHO about it on 24th November. We heard plenty about it on the 25th and it was named Omicron on the 26th. Overall covid case numbers in South Africa had already started rising notably, signalling a new wave, by the time they were in a position to inform the world about it.

I dont want to answer your other questions because I am tired and because infection to death time intervals vary across a range, and because not every case that is Omicron will be identified as Omicron, and because which age groups are first affected by large case numbers of the variant has an impact on initial death quantities and timing.
 
South Africa told the WHO about it on 24th November. We heard plenty about it on the 25th and it was named Omicron on the 26th. Overall covid case numbers in South Africa had already started rising notably, signalling a new wave, by the time they were in a position to inform the world about it.
That recent oh, well. I am worrying ahead of myself then.
I dont want to answer your other questions because I am tired
No worries, thanks for the above.
and because infection to death time intervals vary across a range, and because not every case that is Omicron will be identified as Omicron, and because which age groups are first affected by large case numbers of the variant has an impact on initial death quantities and timing.
Aha, thanks ..
 
We are already into the period where worrying in a pro-active way is sensible. The estimated doubling time for this variant is very low and so its rise is expected to be rapid.
 
The news from Gauteng has gone a little quiet ... here is an updated version of that graph that appears not to show the exponential rise continuing at the same rate.



However as she points out, it could be related to testing capacity.

 
Two hypotheses about why Omicron emerged in South Africa. Unsurprisingly, Merck deny it has anything to do with their clinical trials of molnupiravir, which began in October 2020. With luck, article should be free to read.
 
Two hypotheses about why Omicron emerged in South Africa. Unsurprisingly, Merck deny it has anything to do with their clinical trials of molnupiravir, which began in October 2020. With luck, article should be free to read.

It's not unfortunately. Would you mind, er, exerpting it here?
 
It's not unfortunately. Would you mind, er, exerpting it here?
Sorry - their coronavirus stuff used to be open access. I don't think there's anything new, it's just in a handy article. It's a bit long, and there's graphs and all, and I don't know how to evade their naughty trackers. You could try archive.ph

Basically they're saying it has probably been around undetected for a year, as it bears more genetic similarity to older strains than to Beta and Delta. Suggestions are that either it came from chronic infection via someone with untreated HIV or evolution accelerated by the use of anti-Covid drugs. Crossover to animals then back again not ruled out but considered unlikely.
 
Two hypotheses about why Omicron emerged in South Africa. Unsurprisingly, Merck deny it has anything to do with their clinical trials of molnupiravir, which began in October 2020. With luck, article should be free to read.

The molnupiravir thing is not a hypothesis, it's just idle speculation.

Given that South Africa has faced the first wave of Omicron infections, it is likely that the variant traces its roots to somewhere in the region, said Richard Lessells, an infectious diseases physician at the University of KwaZulu-Natal in Durban.

A South African research team, which included Lessells, discovered an untreated HIV patient late last year who was infected with Covid-19 for more than six months and gave rise to a string of mutations that affected the spike protein, the part of the virus where most of Omicron’s adaptations are located. A UK study observed a similar process in a Covid patient with blood cancer.

The immune response of an untreated HIV patient would be “too weak to clear the virus but strong enough to drive the process of evolution”, explained Lessells. He said this process would allow coronavirus to mutate without being “picked up” as many of these patients are asymptomatic and therefore do not get tested.

“This evolutionary pathway is likely to be rare but it’s a plausible reason for the emergence of Omicron,” said Lessells.

More than half of the world’s 37.7m HIV sufferers are in east and southern Africa. In South Africa alone, around 1.9m individuals have HIV that is undetected, untreated or poorly controlled, according to UNAIDs, the UN programme on HIV/Aids.

Jonathan Li, director of the Harvard/Brigham virology specialty laboratory in Boston, said it was “striking” that two variants of concern — Beta and Omicron — had arisen in southern Africa, a region with “large numbers of immunosuppressed individuals as a result of HIV infection”.

“The collision of high case numbers, low vaccine availability and decades of an HIV crisis means that the chance immunocompromised individuals have been carrying Covid for a while is very high,” said Otto. “It’s important to recognise that many of these health crises are not independent of one another.”

Another theory about how Omicron emerged in southern Africa has been advanced by William Haseltine, a virologist who has speculated that mutations could have been caused by Merck’s Covid-19 antiviral pill. He noted that South Africa was among the locations chosen for clinical trials of the drug molnupiravir, which began in October 2020.

UK and EU regulators have already authorised molnupiravir for emergency use but some scientists, including Haseltine, have warned that its mutagenic properties could, under certain circumstances, create more dangerous variants. These concerns were also raised by external experts at a US Food and Drug Administration meeting last week.

“That is a very heavily mutated virus and that is the kind of patterns you see with molnupiravir,” Haseltine told the Financial Times. “And the timing is right. I’m not saying it happened, but it could have happened.”

Merck told the FT that Haseltine’s “unfounded allegation has no scientific basis or merit”.

“There is no evidence to indicate that any antiviral agent has contributed to the emergence of circulating variants,” said a Merck spokeswoman.

As more genomes are sequenced worldwide, researchers are beginning to piece together the origins of Omicron. Each genome from areas with limited genomic surveillance coverage helps understand the “missing branches” of Omicron’s phylogenetic tree, said Lessells. More than 1,300 Omicron sequences have been uploaded to Gisaid, a global genomics repository, since November 22.

Recent sequencing has shown the idea that Omicron was spreading undetected for some time in an area not sampled by genome testing to be “increasingly implausible”, according to Stuart Ray, professor of medicine at Johns Hopkins University.

“As we get more sequencing data, it is clear that the genomes are tightly clustered,” explained Ray. “There would be more diversity if it had been spreading undetected.”

The theory that the mutation arose in animals before being passed back to humans “is not completely implausible but there is very little reason to believe that happened”, Ray added. “When you look at the passage of human viruses in animals, they accumulate mutations that are suited to that host, not to humans.”

Back in South Africa, medics and scientists stressed that, regardless of how Omicron emerged, richer, western nations should learn the lessons of its evolution.

“We’ll never find patient zero,” said Prof Ian Sanne, director of the HIV research unit at the University of the Witwatersrand. “But we must prevent history from repeating itself.”

“For the pandemic to end, we have to...address all regions of the world at the same time. It worries me that Africa could be the last in line for an Omicron-specific vaccine, if it’s necessary.”
 
Yeah we arent likely to get to the bottom of that variants exact origins, and much will likely remain in the realm of speculation rather than fact.

However its fair to say that more broadly, experts and authorities are aware of the potential role of immunocompromised patients and certain drug treatments in the evolution of viral strains with certain properties. Hence both SAGE and Whitty comments about antivirals in recent weeks.
 
From the BBC live updates page: https://www.bbc.co.uk/news/live/uk-scotland-59607055

The first minister says there are now 110 confirmed cases of Omicron.

Ten days ago there were nine, she says.

The first minister says Omicron is rising exponentially - the fastest exponential growth we have seen in the pandemic so far and says the variant is doubling every two and three days and is closer to two.

She says if that continues, Omicron will overtake Delta as the dominant strain in Scotland and adds that this is likely to happen within days.

Ms Sturgeon says that the R number associated with Omicron is likely to be well over 2, close to 3.

She estimates the R number overall in Scotland is likely to rise above 2.

And she says that it is no longer a question of if we are facing a surge in cases, but when.

She says Omicron is more capable of infecting people who have previously been infected.

And she says vaccines may be less efficient in fighting the virus.

Ms Sturgeon adds that we do not yet know if Omicron causes more, or less, serious illness.
 
Early estimates but worth highlighting:


▪ the risk of household transmission using routine testing data (adjusted odds ratio of transmission from an Omicron index case compared to a Delta index case 3.2 (95% CI 2.0-5.0))
▪ the risk of a close contact becoming a secondary case (adjusted odds ratio 2.09 (95% CI: 1.54-2.79))
▪ the household secondary attack rate using routine contact tracing data (Omicron, 21.6% (95% CI: 16.7%-27.4%), Delta 10.7% (95% CI: 10.5%-10.8%)

The growth advantage is also visible in the community testing data. The proportion of cases with SGTF (now highly predictive of Omicron) continues to grow rapidly. The estimated growth rate of Omicron based on adjusted SGTF counts is 0.35 per day. If Omicron continues to grow at the present rate, Omicron case numbers are projected to reach parity with Delta cases in mid- December.

There is currently no evidence of increased reinfection risk at the population level, but preliminary analyses indicate approximately three- to eight-fold increased risk of reinfection with the Omicron variant.

The Variant Technical Group reviewed the available neutralisation data from published international and internal UK studies (UK Health Security Agency, University of Oxford). UK data will be published as soon as possible and cited here when available. Across 5 preliminary live virus studies (3 international and 2 UK), there was a 20- to 40-fold reduction in neutralising activity by Pfizer 2-dose vaccinee sera for Omicron compared to early pandemic viruses. There was at least 10 fold loss of activity when compared to Delta; in both UK studies this was over 20 fold. A greater reduction in activity was seen for AZ 2- dose sera, and for a high proportion of such sera, neutralising activity fell below the limit of quantification in the assay. An mRNA booster dose resulted in an increase in neutralising activity irrespective of primary vaccination type, including an increase in the proportion of samples that were above the limit of quantification. This is true regardless of which vaccine was used for the primary course. These data are from the early period after the booster and data are urgently required on the durability of neutralising activity.

Early estimates of vaccine effectiveness (VE) against symptomatic infection find a significantly lower VE for against Omicron infection compared to Delta infection. Nevertheless, a moderate to high vaccine effectiveness of 70 to 75% is seen in the early period after a booster dose. With previous variants, vaccine effectiveness against severe disease, including hospitalisation and death, has been higher than effectiveness against mild disease. It will be a few weeks before effectiveness against severe disease with Omicron can be estimated, however based on this experience, this is likely to be substantially higher than the estimates against symptomatic disease. The duration of restored protection after mRNA boosting is not known at this juncture.

Updated variant risk assessment as a result:

 
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Does anyone know if the risk of fomite transmission is increased with Omicron? Had a quick Google and couldn't find anything on it specifically.
 
I have no Expertise whatsoever but if the increased transmission of Omicron is because of changes in the spike protein as we are being told then I would assume that regardless of the delivery method the risk will be higher
Though of course its widely held that the main delivery method is via aerosol.
 
Does anyone know if the risk of fomite transmission is increased with Omicron? Had a quick Google and couldn't find anything on it specifically.

Nobody will know yet, but I wouldn’t image the latest changes are enough to fundamentally change this kind of thing.

Luckily, it's bad enough with covid being airborne!!!
 
Nobody will know yet, but I wouldn’t image the latest changes are enough to fundamentally change this kind of thing.

Luckily, it's bad enough with covid being airborne!!!
Indeed! Thanks - I think there'll be a lot more mask-wearing but Joe Public hasn't been worrying about fomites as they seem pretty low risk with previous variants. Can't remember when I last saw someone using hand sanitiser.
 
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