B.1.1.529 Omicron variant

[bob sterman]

When it comes to Delta vs Omicron numbers.

Sorry if this is a daft question - but can you get both at once? If someone is in the first few days of Delta infection - is there any reason they couldn't get a dose of Omicron at the same time?

Suppose you wouldn't get s-gene dropout on the PCR though.

[jdc]

Rare, but yeah.

https://theconversation.com/coronavirus ... nts-154748

Scientists in Brazil recently reported that two people were simultaneously infected with two different variants of SARS-CoV-2, the virus that causes COVID-19. This co-infection seemed to have no effect on the severity of patients’ illness, and both recovered without needing to be hospitalised.

https://www.cnbc.com/2021/07/12/belgian ... -time.html

Experts have presented a case study of a 90-year-old woman in Belgium who was simultaneously infected with both the alpha and beta strains of Covid-19.

[Trinucleus]

While we're asking questions...

If Omicron is more contagious, do we know if 2m social distancing is still safe? Is the safe time for close contact shorter?

[lpm]

All official numbers are several days old and Omi's doubling time is fast. Call it two doublings since the 15,000 number = 60,000. That's a generous estimate of Omicron cumulative infections right now. No way can it be 200,000.

Tom Chivers on twit gets there via assuming 6 day lag, 2 day doubling time, hence 3 doublings.

My "model" started off with a 3.5 day doubling time. Which is much more consistent with European data. But the UK does indeed calculate to currently doubling every two days...

It makes rather a big difference. 2 days, in a highly vaccinated country with well over 20 million boosters? The NHS is overwhelmed by the cases on 31 Dec, rather than 11 Jan.*


* by this I mean the case load by this date guarantees the coming collapse after a couple of weeks lag, rather than the collapse happens on this date. Assuming not intrinsically more mild.

[lpm]

I reckon we've got 1 week left to act, at this doubling rate, if cases are indeed that high.

Full lockdown by 20 Dec, bringing cases under control by 27 Dec. It takes a while for household infections to work through a family, hence the lag.

Depends a bit on how well voluntary lockdown will happen this week. Today was encouraging. Deserted bars and theatres this week will buy us some time. Plan B is pathetic but the public are sensible.

[lpm]

Worth re-reading our thread from March 2020.

Football and theatres ceased long before govt action. Things just shut down. The equivalent this time would be football fixtures for the coming weekend being cancelled.

I struggle to believe doubling is 2 days but that's the maths. I hope it's milder and suspect it might be, but that's not enough.

It could happen faster than we think. I've done my Brexit style stockpile shopping. Have you? Time to accept Herainestoldism and prepare for a month of total lockdown.

[dyqik]

I struggle to believe doubling is 2 days but that's the maths. I hope it's milder and suspect it might be, but that's not enough.

And milder but more virulent can mean more deaths per week, and higher hospitalization rates. Even before you take account of more idiots deciding that they definitely don't need to take precautions because it's milder.

[jdc]

I struggle to believe doubling is 2 days but that's the maths. I hope it's milder and suspect it might be, but that's not enough.

And milder but more virulent can mean more deaths per week, and higher hospitalization rates. Even before you take account of more idiots deciding that they definitely don't need to take precautions because it's milder.

'scuse the pedantry, but I think you might mean contagious rather than virulent.

[dyqik]

I struggle to believe doubling is 2 days but that's the maths. I hope it's milder and suspect it might be, but that's not enough.

And milder but more virulent can mean more deaths per week, and higher hospitalization rates. Even before you take account of more idiots deciding that they definitely don't need to take precautions because it's milder.

'scuse the pedantry, but I think you might mean contagious rather than virulent.

Probably, yes.

More likely to go viral.

[Herainestold]

It could happen faster than we think. I've done my Brexit style stockpile shopping. Have you? Time to accept Herainestoldism and prepare for a month of total lockdown.

Two to three months.

[Woodchopper]

Interesting thread on second generation lineages: https://twitter.com/peacockflu/status/1 ... 71304?s=21

[Woodchopper]

Thread on whether Omicron will replace Delta: https://twitter.com/trvrb/status/147042 ... 30274?s=21

tl;dr they might coexist.

[Woodchopper]

Waning COVID super-immunity raises questions about Omicron
The pairing of SARS-CoV-2 infection and vaccination against it confers powerful protection, but data from Israel show that that protection gradually declines.

https://www.nature.com/articles/d41586-021-03674-1

[lpm]

Thread on whether Omicron will replace Delta: https://twitter.com/trvrb/status/147042 ... 30274?s=21

tl;dr they might coexist.

But lockdown.

Delta has been rising slightly. Call it R=1.1. We now introduce Plan B, probably B+ due to voluntary action. It becomes R=0.9. I would expect further action to take it to R=0.7.

Why isn't he taking this into account? Delta declines while Omicron explodes.

His starting premise of waning immunity against Delta doesn't seem valid in the real world of boosters.

[Woodchopper]

Thread on whether Omicron will replace Delta: https://twitter.com/trvrb/status/147042 ... 30274?s=21

tl;dr they might coexist.

But lockdown.

Delta has been rising slightly. Call it R=1.1. We now introduce Plan B, probably B+ due to voluntary action. It becomes R=0.9. I would expect further action to take it to R=0.7.

Why isn't he taking this into account? Delta declines while Omicron explodes.

His starting premise of waning immunity against Delta doesn't seem valid in the real world of boosters.

He’s based in the US, different situation there. Probably isn’t thinking about the UK.

[lpm]

Oh f.ck.

Two Pfizers only give 70% protection against hospitalisation. Apparently.

That's not good.

We expect the 3rd dose to take it back up to the previous protection level. And most of the elderly have had their boosters.

But fundamentally, we in the UK saw a steady high load of hospitalisations over the last few months with Delta, as a result of the constant case load. Restoring Omicron protection to that level isn't enough.

Unless Omicron is inherently milder, an official case figure of, say, 250,000 a day - 5x the ongoing Delta level - then hospitalisations will be:

- triple dosed elderly at 5x the level of the previous few months
- double dosed middle aged at a much higher rate than the last few months, because they've dropped from c.90% protection against hospitalisation to 70%. And two AZs is probably worse than two Pfizers.
- a few handfuls from the partly vaccinated young. Getting them boostered isn't all that exciting in hospitalisation terms, it's a reduction in transmission play
- plus the unvaccinated who will clog up the hospitals in their usual way

[lpm]

This thread is getting praise.

https://twitter.com/JamesWard73/status/ ... 3643319305

However it's wrong.

Why? Because it confuses comparisons of Omicron vs Delta with Omicron vs original unvaccinated.

The starting point for every analysis should be the Delta status quo. We know exactly what November 2021 looked like - basically constant cases, constant hospitalisations, constant deaths.

So simply add Omicron vs Delta effects on top of that. Never go back to original unvaccinated "natural" numbers.

[lpm]

Worth re-reading our thread from March 2020.

Football and theatres ceased long before govt action. Things just shut down. The equivalent this time would be football fixtures for the coming weekend being cancelled.

• Premier League match tonight cancelled, Brentford vs some mediocre non-entities

• West End performances cancelled for The Lion King, The Life of Pi, Comedy of Errors

• Pantomimes cancelled in Brighton, Milton Keynes, Coventry, Pembrokeshire and St Andrews

[bob sterman]

• Premier League match tonight cancelled, Brentford vs some mediocre non-entities

Although that is because of loads of COVID cases among the mediocre non-entities - not for the fans!

[Woodchopper]

This thread is getting praise.

https://twitter.com/JamesWard73/status/ ... 3643319305

However it's wrong.

Why? Because it confuses comparisons of Omicron vs Delta with Omicron vs original unvaccinated.

The starting point for every analysis should be the Delta status quo. We know exactly what November 2021 looked like - basically constant cases, constant hospitalisations, constant deaths.

So simply add Omicron vs Delta effects on top of that. Never go back to original unvaccinated "natural" numbers.

I think the thread exposes the limits of the ability of people to use Twitter to explain complex ideas. I found the thread difficult to follow. It might have been better if he written it up with paragraphs in a blog.

[Sciolus]

• Premier League match tonight cancelled, Brentford vs some mediocre non-entities

Although that is because of loads of COVID cases among the mediocre non-entities - not for the fans!

Same with the plays. It would be nice if they were closing as a preventative measure; instead they're closing because the virus is ubiquitous.

[raven]

I struggle to believe doubling is 2 days but that's the maths.

Is faster doubling just down to higher transmission (1 person infecting more people) or is it that plus slightly shorter incubation? I read somewhere yesterday that omicron seemed to kick in 3 days post exposure. It was typically 5 days originally, wasn't it? So maybe that explains it.

Anyhow, it's certainly doubling pretty quickly in the under 60s where I am:

Screenshot 2021-12-14 How many coronavirus cases are there in my area.png (60.13 KiB) Viewed 34360 times

If my sister's experiance is anything to go by, that might be schools. They've been getting sporadic cases all term, but it seems like it's taking off again, whether that's omicron or just colder weather/kids snotty from other germs and more contagious I don't know. Two kids in nephew's class positive over the weekend, nephew this morning.

[Woodchopper]

I think lpm mentioned this earlier

Findings:
1. Two-dose Pfizer-BioNTech vaccination provides significant protection against hospitalisation in individuals with Omicron variant infection

Discovery Health’s research on the effectiveness of two-dose Pfizer-BioNTech vaccination in preventing severe disease and hospitalisation as a result of Omicron variant infection was carried out by Discovery Health’s actuarial team in collaboration with leading scientists at the South African Medical Research Council.

“We used a test-negative design methodology to establish the Pfizer-BioNTech COVID-19 vaccine’s real-world effectiveness against hospital admission from Omicron infection,” says Shirley Collie, Chief Health Analytics Actuary at Discovery Health. “We carried out three carefully constructed sensitivity analyses, with consistent results across each analysis supporting the veracity of our findings. These findings were reviewed by scientists at the SAMRC with whom we have collaborated in multiple areas of our pandemic-related research to date.”

The result shows that vaccinated individuals who received two doses of the Pfizer-BioNTech vaccine had 33% protection against infection, relative to the unvaccinated, in the first weeks of South Africa’s Omicron-driven fourth wave. This represents a significant drop from the 80% protection against infection afforded during the earlier period, probably on the basis of lower antibody susceptibility, following the extensive spike protein mutations in the Omicron variant.

Encouragingly, though, the result shows that these same vaccinated individuals who received two doses of the Pfizer-BioNTech vaccine had 70% protection against hospital admission in this same time period. While protection against hospital admission reduced from the highs of 93% in South Africa’s Delta-driven wave, 70% is still regarded as very good protection.

President of the SAMRC, Professor Glenda Gray, said, “We are extremely encouraged by the results of Discovery Health’s analysis. It is extremely important to be able to demonstrate to the public that in a real-world setting – in the presence of a highly transmissible new COVID-19 variant – the Pfizer-BioNTech vaccine provides good protection against severe disease and hospitalisation.”

Furthermore, the analysis demonstrates that protection against hospital admission is maintained across all ages, in people from 18 to 79 years, with slightly lower levels of protection for the elderly (67% in people aged 60 to 69 and 60% for people aged 70 to 79). Protection against admission is also consistent across a range of chronic illnesses, including diabetes, hypertension, hypercholesterolemia and other cardiovascular diseases.

2. Omicron reinfection risk significantly higher compared to prior variants

“With each successive wave of COVID-19 infection in South Africa, we have investigated the durability of immunity following previous infection with COVID-19 – in other words, the risk of reinfection,” explains Collie.

“Overall, the risk of re-infection (following prior infection) has increased over time, with Omicron resulting in significantly higher rates of reinfection compared to prior variants.”

People who were infected with COVID-19 in South Africa’s third (Delta) wave face a 40% relative risk of reinfection with Omicron.

People who were infected with COVID-19 in South Africa’s second (Beta) wave face a 60% relative risk of reinfection with Omicron.

“While individuals who had a documented infection in South Africa’s first wave, and therefore were likely to have been infected with the SARS CoV-2 virus carrying the D614G mutation, face a 73% risk of reinfection relative to those without prior documented infection,” adds Collie.

3. Risk of severe disease and hospitalisation significantly lower in Omicron infection compared to prior variants

Discovery Health has investigated the Omicron variant’s clinical impact relative to other SARS-CoV-2 variants.

“Epidemiological tracking shows a steep trajectory of new infections, indicating Omicron’s rapid spread, but so far with a flatter trajectory of hospital admissions, possibly indicating lower severity,” explains Dr Noach. “This lesser severity could, however, be confounded by the high seroprevalence levels of SARS CoV-2 antibodies in the general South African population, especially following an extensive Delta wave of infections.”

Collie adds, “Adults are experiencing a 29% lower admission risk relative to South Africa’s first wave of infection, dominated by D614G, in early 2020. Furthermore, hospitalised adults currently have a lower propensity to be admitted to high-care and intensive-care units, relative to prior waves.”

4. Preliminary observations on Omicron experience in children

“Notwithstanding the fact that children continue to show a very low incidence of severe complications following COVID-19, Discovery Health’s data indicates that children under age 18 have a 20% higher risk of admission for complications of COVID-19 when infected with Omicron,” says Collie. “This is early data and requires careful follow-up. However, this trend aligns with the warning from South Africa’s National Institute for Communicable Diseases (NICD) in recent days that during South Africa’s third wave of infection (June to September 2021) they had seen an increase in paediatric admissions and now, in the fourth wave, they are seeing a similar increase in admissions for children under five years of age. Anecdotal reports from hospitals in South Africa indicate that most COVID-19 diagnoses in children admitted to hospital are co-incidental – many children who are admitted for non-COVID-19-related conditions, and who are not experiencing COVID-19 complications, test positive for COVID-19 on routine screening tests.”

It is also important to note that Discovery Health’s analysis shows that the risk of children testing positive for COVID-19 infections is significantly lower than in adults.
“Children were 51% less likely to test positive for COVID-19 relative to adults in the Omicron period and, overall, the risk of children being admitted to hospital for COVID-19 complications remains low,” Collie adds.
Where children require admission for complications of COVID-19, the primary diagnoses are bronchiolitis and pneumonia, often with severe gastrointestinal symptoms and dehydration.
“The majority of children present with mild disease, with symptoms such as a sore throat, nasal congestion, headache and fever that resolves within three days,” adds Dr Noach, based on anecdotal consensus sourced from the treating healthcare professionals.

https://www.discovery.co.za/corporate/news-room

[Woodchopper]

High levels of previous exposure to three previous waves of coronavirus infection in South Africa may explain the relatively low levels of hospitalisation and severe disease in the current outbreak of the Omicron variant, rather than the variant itself being less virulent.

The suggestion was made by the vaccine expert Shabir Madhi of the University of the Witwatersrand, who has led vaccine trials in the country. He warned that South Africa’s experience of Omicron might not be a reliable indicator for how the Omicron outbreak unfolds in other countries.

The same message was echoed by the head of the World Health Organization (WHO), Tedros Adhanom Ghebreyesus, who said it was “wrong for people to consider Omicron as mild”.

Other senior WHO officials, warning that the peak of Omicron could be weeks away as it spread rapidly, added that current evidence suggested vaccines were not failing to protect against Omicron altogether, and did offer some degree of protection.

In a lengthy interview with the Global Health Crisis Coordination Center, Madhi cited a recently completed seropositivity survey – the percentage of population who have already been infected – in Gauteng province, which has been at the centre of the Omicron outbreak, that suggested 72% had experienced a previous infection of coronavirus.

That is well over three times the rate of previous infections detected by a similar survey during the Beta variant outbreak a year ago where seropositivity was 20%.

While Madhi said emerging evidence pointed to the fact that Omicron was both more infectious and more able to evade antibody protection, he suggested other mechanisms at work in acquired immunity through infection could explain the lower levels of hospitalisations and severe illness.

[...]

“The evolution of the Omicron variant is coming at a very different stage of the pandemic,” said Madhi. “That is important to keep at the back of our minds when we see what is unfolding in South Africa and what we might see in other settings, which might have a very different epidemiology.”

“In the South African much of the immunity that currently exists is largely because of the prior infection that has taken place during the first three waves,” he added. “In a survey that fortuitously just ended in [Gauteng province] on Friday what we demonstrate is that the seropositivity in Gauteng is about 72%.

“That is important to keep in the back of our mind when we see what is unfolding in South Africa and what we might expect in other settings.”

Addressing the issue of whether Omicron is “milder” than other previous variants, Madhi said the high levels of previous exposure meant that experts were “simply unable to make a meaningful head-to-head comparison of virulence with Omicron in comparison with the other variants.

“[That is] imply because of the underpinning of immunity that currently exists which is different to what existed in the past, and that immunity is going to bring about some change in the clinical course of the infection, including the likelihood of infection progressing to severe disease.”

“What is quite fascinating is that taking the rate of infection per 100,000 and comparing that to the hospitalisation rate as well as the death rate, the hospitalisation rate is much more muted compared with what was the equivalent case rate in the first three waves that transpired.

“So it tells us something is at play when the high force of infections with Omicron is not materialising in terms of severe disease and deaths in large numbers.”

Citing evidence of Omicron’s ability to evade antibody protection he suggested data was “congregating” that immunity from T cells might be driving protection against more severe disease.

[...]

Madhi’s argument appears to have the support of some other experts. Tulio de Oliveira, who runs two gene-sequencing institutes in South Africa, told CBS over the weekend: “You have large pockets of population immunity … We’re going to have to tease apart if the mild cases are due to young people getting infected or if the previous population immunity from infection and vaccination are responsible for decreasing the number of hospitalised individuals.”

https://www.theguardian.com/world/2021/ ... dApp_Other

[raven]

Excellent links as always Woodchopper, what would we do without you posting such informative stuff.