Since the Omicron variant was first identified as a variant of concern, everyone wants to understand severity. An initial study in South Africa suggests Omicron is less severe, whereas a UK study finds no difference. My view? Still too early too tell.

There are two main published analyses of severity so far (neither peer reviewed) based on substantial population level data from South African and the UK. But even substantial data is still very early in this outbreak.

From South Africa, Discovery Health (South Africa’s largest private health insurance administrator, with 3.7 million clients) has analysed their customer data. Their comments are:

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.

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

Whereas from the UK, the Imperial College UK also looks at infectiousness, but also severity. This analysis is based on a total of 208,971 S+ and 15,063 S- cases with complete data (this is using the PCR test, which has a specific “S-” to identify Omicron, which they have analysed as being very closely matched to  full genetic analysis).  For hospitalisation rates they reach this conclusion:

Hospitalisation and asymptomatic infection indicators were not significantly associated with Omicron infection, suggesting at most limited changes in severity compared with Delta.

This comment is based on an outcome that Omicron cases are 95% as likely to be in hospital as Delta cases, with a potential range around that number of (0.61-1.47).

So the South African study suggests that a vaccinated individual is more likely to be hospitalised by Omicron than Delta (30% chance of hospitalisation, compared with 7%) but that after adjusting for vaccination status, adults are experiencing a 29% lower admission risk compared with earlier waves, and once hospitalised, less likely to be seriously ill. The Discovery study doesn’t give statistical significance.

The UK study, on the other hand, suggests no change in hospitalisation rates.

Hospitalisation rates could look lower in these studies than reality for a few reasons:

  • It is still early days. The median delay between a person becoming ill with COVID-19 and requiring a hospitalisation is 6 days (NSW Health). In a situation of rapidly growing cases, hospitalisation rates will lag case numbers considerably.
  • The first people infected in a population are likely to be younger and healthier (more likely to be out nightclubbing or socialising generally), so less likely to have severe disease (both studies tried to correct for this)
  • If you are more likely to get infected, but be protected by your prior immunity, the hospitalisation rates will look lower than they would be for a non vaccinated/non infected person (more on this below).

Hospitalisation rates could also look higher in these studies than reality because:

  • The hospitalisation rates appear to include everyone in hospital who is positive for Covid19. Some of those are not ill with Covid, just happen to be in hospital for something else, and in a rapidly spreading situation, they could be a higher proportion of the total than they will be later

This twitter thread from Epidmiologist Marc Lipsitch was very helpful in understanding these two studies, if you’d like to read more.

This picture from @nataliexdean explains  one aspect of why analysing severity is hard, now that we have the complication of imperfect immunity (protecting against severe infection, but not reinfection).

To measure severity in a real outbreak, you need to look at the proportion of cases that end up being hospitalised or worse. Simple, right? Not quite. In the original outbreaks around the world, everyone was susceptible. So the severity of the original strain of Sars Cov2 could be measured based on the whole population. But now, every where around the world has some combination of previous infection or vaccination. In general, those who have been vaccinated are those who were (pre vaccination) more likely to be at higher risk of severe disease. So the Delta outbreaks in the UK in 2021 ended up with lower infections, and less severe disease, because higher risk people had been vaccinated. But Omicron appears to infect everyone, whether they have some immunity (through vaccination or previous infection), or have no immunity. If those people who are somewhat immune end up with a less severe disease, then it looks as if the variant is less severe overall.

But it might just be that vaccination averts the serious disease, but those without immunity end up just as sick.  So Omicron could be less severe in everyone who gets infected. But if twice as many people get infected with Omicron as would have got infected with Delta, then Omicron might have half the severity but the same number of people get seriously ill.

So to get a really good measure of severity of a disease, you need to understand the immunity status of all cases, and compare them with severity. Both studies attempted to do this, but it isn’t easy.

For me, deep diving into these studies confirms that you are much safer with vaccination, particularly if it is an mRNA vaccine, and especially if you have had a third dose and/or previous infection. It does seem plausible that the disease could be a little less likely to cause hospitalisation than Delta was. But as I noted in my last post, hospitals could still be overwhelmed even with a milder disease.

I’ve found that most commentators seem to gravitate to the study that confirms their initial views. I’ve tried not to be influenced by my initial thinking, but for transparency, my initial thought was that the new virus variant should be assumed to be equally severe unless proven otherwise.

Links

As always, Ed Yong, from the Atlantic has the piece we need to read right now. Go and read the whole thing (and everything Ed Yong writes) but here are two very relevant quotes:

In any case, America is not prepared for Omicron. The variant’s threat is far greater at the societal level than at the personal one, and policy makers have already cut themselves off from the tools needed to protect the populations they serve. Like the variants that preceded it, Omicron requires individuals to think and act for the collective good.

And even if Omicron is milder, greater transmissibility will likely trump that reduced virulence. Omicron is spreading so quickly that a small proportion of severe cases could still flood hospitals.

And a quick survey of what is happening around Europe as Omicron spreads like wildfire.

Spain (81% fully vaccinated) is having an emergency national cabinet meeting next week

Spanish Prime Minister, Pedro Sánchez, will hold a virtual Conference of Presidents next week in view of the advance of the sixth wave of the coronavirus, which has put Spain at very serious risk of contagion on the eve of the Christmas holidays. The meeting is due to be held on Wednesday 22 December, according to government sources.

Denmark (78% fully vaccinated) reintroduces serious restrictions but without lockdown

The minority cabinet proposed closing zoos, theme parks, theaters and cinemas to halt activity in society and break contamination chains, Prime Minister Mette Frederiksen told reporters in Copenhagen on Friday. It will also propose compensation for businesses affected by new restrictions, she said.

Ireland (77% fully vaccinated) introduces an 8 pm curfew for hospitality

Venues should run at reduced capacity – for indoor venues it is 50% of capacity, or 1,000 people (whichever is lower) and outdoor events should be limited to 50% or 5,000 people (whichever is lower).

Netherlands (75% fully vaccinated) reintroduces a nationwide lockdown

All non-essential stores, bars and restaurants will be closed until mid-January, caretaker Prime Minister Mark Rutte said at a hastily arranged press conference on Saturday night.

Paris (73% fully vaccinated) has cancelled its traditional New Year Fireworks

Paris on Saturday said it was cancelling its traditional New Year fireworks as Europe braced for tighter curbs to rein in the spread of the new strain of the coronavirus fuelling a resurgence in Covid-19 cases worldwide.

Germany (70% fully vaccinated) tightens restrictions for the unvaccinated

Merkel and Scholz told reporters in Berlin that under the new rules, the unvaccinated will be excluded from nonessential stores and cultural and recreational venues. They made the announcement following a meeting with the governors of Germany’s 16 states.

Merkel said parliament will also consider imposing a general coronavirus vaccine mandate as part of the country faces a fourth wave of infections. Germany’s Robert Koch Institute for infectious diseases (RKI) says the nation once again Thursday exceeded 70,000 new cases in a 24-hour period.

England (69% fully vaccinated) reintroduces some restrictions

From Friday 10 December the legal requirement to wear face masks in shops and on public transport will be extended to most public indoor venues, including theatres and cinemas. But you will not have to wear masks in cafes, restaurants or pubs. From Monday 13 December people have been urged to work from home. “Go to work if you must but work from home if you can,” Johnson said.

Switzerland (66% fully vaccinated) has tightened its rules for the unvaccinated

In Friday’s meeting, the Council has decided to tighten up measures for unvaccinated and unrecovered people in the country by replacing the 3G rule with a 2G rule. This means that in places like restaurants, cultural, sporting and leisure venues and events where vaccinated, recovered and tested persons have been eligible to enter, now only those vaccinated and recovered will be able to do so.  The requirement to wear a mask in these places remains an obligation.

Meanwhile here in NSW (79% fully vaccinated) we are “standing tall” against the virus

Mr Perrottet reiterated his stance that the government would tailor its response as the outbreak unfolded instead of reintroducing restrictions as a pre-emptive measure. The low number of current ICU presentations was positive, he said.

“When we believe there’s evidence in front of us we need to potentially tighten restrictions we will,” he said. It was “strongly recommended” to wear a mask in most settings, Mr Perrottet said, but he placed the onus on people taking “personal responsibility” for their health.

“And the people of New South Wales are doing just that. The government can’t do everything,” he said.

This op-ed in the Sydney and Melbourne papers today (from three epidemiologists including the Director of the Doherty Institute) expresses my view of what Australia should be doing with public health policy right now.

Early data on vaccines indicate that their protection is greatly reduced for protection against infection in people who have received a two-dose course, but that boosters can restore immunity. Protection against severe disease is likely to be maintained to a greater degree but we still need more information about how much. We therefore need to put the brakes on transmission by restoring some restrictions to allow scientists to gather, analyse and report information on these key unknowns.

If it turns out that Omicron causes much less disease than Delta, the most we will have lost is a few weeks of unrestricted gathering. In the reverse scenario, we will have prevented many thousands of transmissions and put ourselves in a much stronger position to defend the health system.
The evidence that will emerge quickly from the other countries a few weeks ahead of us in their Omicron waves will be invaluable. Compared to the northern hemisphere, we have the summer season and outdoor living in our favour, but we should not put our faith in sunny optimism when it comes to managing the next chapter of the pandemic.

Life Glimpses

As I hoped, I did manage to see Hamilton this week. And it completely lived up to my expectations. Seeing it live really brought home to me how well constructed a show it is – not just great songs, not just a great story, but a coherent whole.

But after that wonderful evening, one of our family was identified as a close contact of a confirmed case, so we’ve all been staying home, and missing a few more of the social occasions we had been looking forward to. While technically those of us who aren’t close contacts are still allowed to leave the house, it doesn’t seem very sensible to do so.  And we had a few  conversations with friends about choosing which social occasion was most worth while and skipping the others to make sure you could get to that one.

On the plus side, all the rapid antigen tests we bought (before our local chemist ran out) have been negative, and I got my booster shot (by sneaking in a bit early).

Bit of Beauty

One of the parties I did manage to get to in the last week had this disco ball, which we all thought looked a bit like a Covid virus.

 

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