Omicron news

[elbows]

NERVTAG minutes November 25th (published on the 29th):

Box

app.box.com

Some quotes:

SA estimates an R-value of 1.9 for B.1.1.529 in Gauteng.

The R-value estimate of 1.9 is occurring against a background of high levels of immunity following the recent wave (wave number 3) of Delta variant infections in SA and an active immunisation programme.

Although there is not yet any direct experimental evidence of immune escape, the genotype and the epidemiology in SA are highly suggestive that B.1.1.529 is an antigenically divergent variant that is able to successfully infect previously infected or vaccinated individuals.

There are currently insufficient data to make any comments on disease severity associated with B.1.1.529.

Conclusion: the subgroup concludes that if introduced into the UK, B.1.1.529 would likely be capable of initiating a new wave of infections. We cannot exclude that this wave would be of a magnitude similar, or even larger, than previous waves.

Conclusion: Although data on disease severity associated with B.1.1.529 are not yet available, a large wave of infections will be accompanied by a wave of severe cases and the subgroup cannot rule out that this may be sufficient to overwhelm NHS capacity

Although computational analyses are ongoing, the multiple mutations observed in theB.1.1.529 spike glycoprotein are likely to render many of the currently available monoclonal antibodies ineffective.

Acceleration of the vaccine boosting campaign should be considered, which might provide some residual or significant VE against B1.1.529, and at a minimum would help control concurrent Delta impact.

 

[Riklet]

This has a darkly familiar ring to it.

View attachment 298891

For alll we know it may well have originated in Nigeria.

Huge population
Plenty of immuno suppressed people
Very low vaccination rate (2%? all that oil money being spent well)
Hard hit already in some areas by Covid but not that much overall
Unlikely to have the testing or sequencing going on that South Africa does

 

[brogdale]

For alll we know it may well have originated in Nigeria.

Huge population
Plenty of immuno suppressed people
Very low vaccination rate (2%? all that oil money being spent well)
Hard hit already in some areas by Covid but not that much overall
Unlikely to have the testing or sequencing going on that South Africa does

Indeed; just like when we were told that Covid emerged/arrived in Jan/Feb 2020 and then it emerged that it had been circulating in France since November 2019.

 

[platinumsage]

Indeed; just like when we were told that Covid emerged/arrived in Jan/Feb 2020 and then it emerged that it had been circulating in France since November 2019.

We were also told it was circulating in Italy and the US in September 2019. I'd treat such claims with some degree of skepticism.

 

[elbows]

We were also told it was circulating in Italy and the US in September 2019. I'd treat such claims with some degree of skepticism.

An added possible factor in those claims about the first origins of SARS-Cov-2 in humans in terms of timing and location was that deliberate disinformation campaigns by China could have been involved in seeding and spreading such details, deliberately muddying the waters.

 

[brogdale]

We were also told it was circulating in Italy and the US in September 2019. I'd treat such claims with some degree of skepticism.

I understood that the epidemiological research stood this up?

 

[elbows]

November 2019 is not September 2019.

Due to lack of surveillance it does make sense to leave a bit of wiggle room in our understanding of the exact timing of the emergence of the original virus. We were only setup to notice once notable impact on hospital admission numbers was noticed, once there had been an explosion of cases somewhere. November 2019 is plausible, especially when we are probably talking about low numbers at that time. Patchy and limited data, even when looking hard retrospectively, makes location even harder to determine than timing. I havent gone looking for any UK-specific studies on that but there was reasonably good anecdotal evidence that there were some sporadic cases in December 2019 that nobody noticed until hindsight was available. Fergus Walsh of the BBC did some articles about that, and was especially interested in the subject since it turns out he may have been an early case himself.

 

[brogdale]

November 2019 is not September 2019.

Due to lack of surveillance it does make sense to leave a bit of wiggle room in our understanding of the exact timing of the emergence of the original virus. We were only setup to notice once notable impact on hospital admission numbers was noticed, once there had been an explosion of cases somewhere. November 2019 is plausible, especially when we are probably talking about low numbers at that time. Patchy and limited data, even when looking hard retrospectively, makes location even harder to determine than timing. I havent gone looking for any UK-specific studies on that but there was reasonably good anecdotal evidence that there were some sporadic cases in December 2019 that nobody noticed until hindsight was available. Fergus Walsh of the BBC did some articles about that, and was especially interested in the subject since it turns out he may have been an early case himself.

Yes, to clarify, I was referring to the November in France evidence, not anything about September; hence my link.

 

[elbows]

This article that involves an interview with the Israeli doctor who caught Omicron and thinks he got it at a conference in London, contains the usual bad framing bullshit that drives me mad. "one of the first people in the world to become infected with the Omicron variant" - NO! Just one of the first people to be confirmed to have this variant, in a country the media pay attention to, at a time when we've actually noticed that this variant exists and when there is much attention being paid towards this variant.

Israeli doctor believes he caught Omicron variant of Covid in London

Exclusive: Cardiologist Elad Maor suspects he caught virus at conference attended by more than 1,200 people

www.theguardian.com

 

[PursuedByBears]

Just messaged my team to say that I won't be in the office for our team day tomorrow because "I think that we need to pause and gather more data before blithely assuming that the Omicron variant is mostly harmless". Let's see how that goes down... I'll wait a couple of days before I tell them I'm not coming to the Christmas meal on Fri 10th as well.

 

[8ball]

Just messaged my team to say that I won't be in the office for our team day tomorrow because "I think that we need to pause and gather more data before blithely assuming that the Omicron variant is mostly harmless". Let's see how that goes down... I'll wait a couple of days before I tell them I'm not coming to the Christmas meal on Fri 10th as well.

I think "mostly harmless" is a long way from most current estimations.

 

[Yossarian]

Cases doubling day-on-day in South Africa seems like an ominous - omicronous? - sign.

South Africa's new COVID cases double in 1 day amid omicron

South Africa’s new cases of COVID-19 have nearly doubled in just one day. The numbers released Wednesday signal a dramatic surge in the country where scientists detected the omicron variant last week.

apnews.com

 

[2hats]

Positivity rate also rocketing (=> climb in case numbers is not an artefact of testing).

Perhaps take the following with a large pinch of salt (certainly unconfirmed/preliminary)...

Separately some Israeli journalists are reporting on a report*, providing numbers that indicate that omicron is around twice as likely to infect (mRNA) vaccinees (two-dose within six months or triple-dosed) as delta has been, whilst the unvaccinated are 2.4 times as likely to get infected by omicron as they were previously by delta. They also claim a similar level of protection to delta for those vaccinees against severe disease, whilst omicron's R is put at around 1.3x that of delta.

* Note: a report of a report, that the Israeli Ministry of Health say they don't have.

 

[2hats]

Possible indication of growing omicron community transmission in England - PCR SGTF rising in recent days.

 

[skyscraper101]

Japan has now reversed its travel ban owing to 'mild' variant

Coronavirus U-turn: Japan partly reverses Covid travel ban as Omicron variant increasingly appears to be ‘mild‘ mutation - City AM

A ban on new incoming flight bookings in Japan has been dropped, the country's government said this morning.

www.cityam.com

 

[Yossarian]

Japan has now reversed its travel ban owing to 'mild' variant

Coronavirus U-turn: Japan partly reverses Covid travel ban as Omicron variant increasingly appears to be ‘mild‘ mutation - City AM

A ban on new incoming flight bookings in Japan has been dropped, the country's government said this morning.

www.cityam.com

Not sure if there's a connection between Japan changing the travel policy and reports of omicron symptom being mild - they reversed the ban on new incoming international bookings after they were accused of abandoning Japanese nationals overseas, the ban on non-Japanese citizens announced Monday is still in place.

 

[gentlegreen]

 

[skyscraper101]

Not sure if there's a connection between Japan changing the travel policy and reports of omicron symptom being mild - they reversed the ban on new incoming international bookings after they were accused of abandoning Japanese nationals overseas, the ban on non-Japanese citizens announced Monday is still in place.

Fair enough. I skim read it and didn't realize it was only a partial reversal.

 

[elbows]

Not sure if there's a connection between Japan changing the travel policy and reports of omicron symptom being mild - they reversed the ban on new incoming international bookings after they were accused of abandoning Japanese nationals overseas, the ban on non-Japanese citizens announced Monday is still in place.

And excessive emphasis on stories about it being 'mild' continue for pretty obvious reasons, people clinging to hope or justifying not taking much action, or trying to defuse some of the more extreme concerns people leap to when fears over a new variant are high.

Indicators from South Africa continue to follow a pretty typical path so far:

Health officials say the new coronavirus variant Omicron has now become dominant in South Africa and is driving a sharp increase in new infections.

Some 8,500 new Covid infections were registered in the latest daily figures.

That is almost double the 4,300 cases confirmed the previous day.

By contrast, daily infections were averaging between 200 and 300 in mid-November, a top South African scientist told the BBC.

The rate of new infections is expected to increase in what is now the beginning of the fourth wave in South Africa, and the national health department says there has also been a slight increase in hospital admissions.

As with previous variants Beta and Delta, the full picture in South Africa will not become clear until "people get so sick that they need to go to hospital" which is generally "three, four weeks later," says Prof Salim Abdool Karim of the Africa Task Force for Coronavirus.

"But the feedback we're getting from the ground is that there's really no red flags - we're not seeing anything dramatically different, what we're seeing is what we are used to," he told the BBC's Newsday programme.

Covid: South Africa new cases surge as Omicron spreads

The new Omicron variant has now become dominant, the country's top medical scientists say.

www.bbc.co.uk

I will want to check hospital data rather than rely on descriptions of a 'slight increase'. And if there continue to be no red flags in regards dramatically different proportion of hospitalisations, then fears of incredible health service pressures will come down to the usual factors we've seen with other variants - it will still be a terrible situation if very large numbers of people catch the virus, so I get most concerned about transmissibility and immune escape rather than the variant being more directly deadly to each individual. And thats the same as the concerns of UK authorities at this stage, the usual numbers game, the usual implications.

 

[2hats]

From ECDC Threat Assessment Brief - Implications of the further emergence and spread of the SARS-CoV-2 B.1.1.529 variant of concern (Omicron) for the EU/EEA – first update, 2 Dec 2021.

The rapid increase of cases, the increase of the effective reproductive number Rt, and the pace of replacement of the Delta VOC by the Omicron VOC in South Africa all suggest that this variant is more transmissible than the Delta VOC, but robust evidence is still lacking and there remains a high uncertainty. Limited evidence gathered from initial cases reported from EU/EEA countries to date also suggests that Omicron may be associated with high transmissibility as high attack rates have been reported among some household contacts.

 

[elbows]

Well this is also a sign that not enough testing is being done, but even so.

 

[elbows]

From ECDC Threat Assessment Brief - Implications of the further emergence and spread of the SARS-CoV-2 B.1.1.529 variant of concern (Omicron) for the EU/EEA – first update, 2 Dec 2021.

Ah its been ages since I looked at any ECDC pandemic documents. Some more quotes from that one:

Current evidence on transmissibility, severity, and immune escape is highly uncertain for the Omicron VOC. However, preliminary data from South Africa suggest that it may have a substantial growth advantage over the Delta VOC. If this is the case, mathematical modelling indicates that the Omicron VOC is expected to cause over half of all SARS-CoV-2 infections in the EU/EEA within the next few months. The greater Omicron's growth advantage over the Delta VOC and the greater its circulation in the EU/EEA, the shorter the expected time until the Omicron VOC causes the majority of all SARS-CoV-2 infections.

Based on the currently available limited evidence, and considering the high level of uncertainty, the overall level of risk for EU/EEA countries associated with the further emergence and spread of the SARS-CoV-2 Omicron VOC is assessed as HIGH TO VERY HIGH.

To date, the Omicron VOC has already been introduced into many EU/EEA countries. Given the current limited evidence around this new variant and the concerns about its immune escape properties in relation to available COVID-19 vaccines and treatments, a multi-layered approach to delay the spread of this VOC in the EU/EEA is needed.
Due to the ongoing circulation of the Delta VOC, EU/EEA countries are urged to give utmost priority towards the vaccination of people initially targeted by COVID-19 vaccination programmes who remain unvaccinated or who are not yet fully vaccinated. Countries should consider a booster dose for people aged 40 years and older, first targeting the most vulnerable and the elderly, and could then consider a booster dose for all adults aged 18 years and older at least six months after completion of the primary series.

Non-pharmaceutical interventions (NPIs) that have proven to be very effective in reducing transmission of infection should continue to be implemented by countries based on an assessment of their epidemiological situation regarding the Delta VOC, and taking into account the uncertainty of the situation regarding the Omicron VOC. Physical distancing measures, ensuring adequate ventilation in closed spaces, the maintenance of hand and respiratory hygiene measures, the appropriate use of face masks, and staying home when ill all remain relevant.

Enhanced contact tracing measures such as backward contact tracing and stricter management of contacts could help slow the establishment of the Omicron VOC in the country.
Genomic surveillance remains of the utmost importance for early detection of the presence of the variant, to enable the following of epidemiological trends and guide containment measures.

Temporary travel-related measures should be carefully considered in light of the latest epidemiological situation, and should be regularly reviewed as new evidence emerges. Such measures might include the testing and quarantining of travellers who have recently returned from affected countries and sequencing cases identified among travellers. Public information around the emerging situation and the public health measures in place for returning travellers from affected areas are important to raise awareness and support the effective implementation of these measures. However, given the increasing number of cases and clusters in the EU/EEA without a travel history or contact with travel-related cases, it is likely that within the coming weeks the effectiveness of travel-related measures will significantly decrease, and countries should prepare for a rapid and measured de-escalation of such measures.

 

[elbows]

 

[2hats]

Preprint of an initial study (NICD/Stellenbosch/others) which suggests that risk of reinfection by omicron for those with natural immunity only (acquired via infection by beta or delta) is 3x higher than for previous VOC.

Population-level evidence suggests that the Omicron variant is associated with substantial ability to evade immunity from prior infection.

DOI: 10.1101/2021.11.11.21266068.

 

[weltweit]

I know Johnston doesn't want the blame for Omicron restrictions over Christmas, but how likely do people think it is that there will be greater restrictions over the Christmas / NY period?

I suppose we have to wait for the assessments on its virulence.

 

[elbows]

Its hard to say. Even without Omicron I would not have wanted to bet against some additional restrictions during winter, although authorities would probably have tried to wait till after Christmas before doing them, making some use of the effect of school holidays in the meantime. And the effects of the booster campaign and prior infections might have meant they got away with only basic stuff rather than the stronger things people often think of when they hear the word restrictions.

With Omicron, it would probably require amost all of the news about Omicrons properties to be very good news in order for the modellers to not come up with results that are extremely worrying to the authorities. But even if all the news is very bad, with resulting scary modelling about the potential consequences of another wave, the timing may yet allow the government to avoid the heavier measures until we progress into January. But the high rates of Delta infection that have been allowed to persist in the UK are an additional complication, robbing authorities of some of the wiggle room that would otherwise be available if an Omicron wave started from scratch rather than building on top of the ugly Delta picture. However the declines seen in hospitalisations, presumably as a result of the young ages of those getting infected the most recently, and also as the result of the booster effects, reintroduces a bit of wiggle room on some key fronts.

So I wouldnt bet on many more restrictions in December, although I could end up saying something different in a weeks time. If the estimates of this variants properties turn out to be especially grim, or the real-world UK data starts to show new alarming properties, even this government might yet feel compelled to act in December. But school holidays arent too many weeks away and the government may fancy their chances of at least being able to drag things out beyond Christmas.

 

[Raheem]

Regardless of the impact of omicron, the government has followed a pattern of delaying as much as they can, and now they also seem to be abandoning the line that they are "following the science". I would expect the intention is to delay past Christmas in all eventualities.

 

[weltweit]

Hi elbows yes those are pretty much my feelings. My son and his mum are planning to visit family in Spain and I am a bit worried about their return trip in case either of them contracts covid and fail their last minute test while they are there. Nothing I can do about it though.

 

[elbows]

Plus dont forget there is already one announced measure that authomatically ramps up if Omicron starts to make up a more notable proportion of cases here. That being the rules where you dont need to self isolate if you are deemed to be a close contact but are vaccinated - these rules that were part of the summer easing have been changed this week so that they do not apply if the person who tested positive is suspected to have the Omicron variant. So there will far be more people told to isolate if Omicron grows, and the relaxed version of those rules are dead if Omicron dominates because every case will be assumed to be Omicron at that point.

 

[StoneRoad]

The gov't will be relying on the vaccines / boosters to do the heavy lifting.
Depiffle seems incapable of pre-empting problems and only reacting, and slowly at that.

Yeah, some harder restrictions - or actually enforcing the existing isolation / mask mandates & maybe extending them to something sensible ? well, I'm expecting something after chrimble.