With new analyses showing lower severity for Omicron cases, what will this mean for our projections? Well obviously this will tend to bring the numbers lower, which is great — but I want to clear up a few misconceptions.
There was some confusion over what our models, which assumed Omicron had equal "baseline" severity to Delta, meant for severity in practice. This leads to around a 40% reduction in realised severity within each age group, because more Omicron cases are breakthrough/reinfections.
There was even a @jpmorgan reanalysis of our projections that just cut the hospitalisation numbers in half, because of reports from South Africa that the hospitalisation rate was lower. We were already predicting that the average hospitalisation rate would be lower (see above).
New papers by @imperialcollege (report 50) show that A&E visits among Omicron cases are reduced by 30-40%. The former would be "70% baseline severity" which looks like this in practice (these plots are outputs from our model btw which we will add to the next preprint version)
There is a really important point, though, that some hugely helpful explainers @JamesWard73@nataliexdean@jburnmurdoch have so far not really focused on (not saying they have overlooked this, just that I haven't seen them tweet about it yet...). And here it is:
The same principle that makes Omicron relatively less severe WITHIN each age/risk group—its better ability to infect those with preexisting protection—will tend to shift the case mix, relative to Delta, AMONG the age/risk groups into those that have relatively better protection.
For a lot of countries, including the UK, this means that the Omicron wave will tend to infect *relatively* more vulnerable older people than the Delta wave, which after all was really primarily in young people.
To the extent that this shift happens, the overall realised severity across all age groups (i.e. the average IHR) will not decrease as much as the above plots suggest.
If the fraction of highly-protected older people infected with Omicron is big enough relative to the very small fraction who got Delta, then in theory this could even increase the average IHR even though it is decreasing within each age group. en.wikipedia.org/wiki/Simpson%2…
If in South Africa, there was higher protection among young people prior to Omicron, this same effect would tend to *decrease* the IHR resulting from Omicron if it was shifting the average Omicron case younger relative to Delta.
The older and vulnerable age groups drive the majority of morbidity and mortality coming out of any model of SARS-CoV-2 transmission. If people exercise even a little bit of caution around their vulnerable/elderly relatives this Christmas, that will make a HUGE difference.
Hence the importance of testing yourself before seeing your friends and family and before / after going out to places where the risk of transmission is high.
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COVID-19 surveillance, England. The most recent 5 days (to 28 Nov) show an increase in S gene target failure in community testing data. An explainer follows. 🧵
But before I go on, I will remind my scientific and media readers that SGTF is only a proxy for Omicron, and is also found in other SARS-CoV-2 lineages. Lineage identity can only be confirmed by sequencing, and longer-term surveillance is required to establish any trend.
I should also add, the fact that there has been an increase in SGTF isn't necessarily surprising — we have 22 confirmed Omicron cases in England as of today, so there was going to be an SGTF signal sooner or later. This isn't meant to be shocking news. Still, good to be aware.
Our paper “Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7” is in Nature today. We find that B.1.1.7, the UK coronavirus variant identified in late 2020, is associated with 55% higher COVID-19 mortality than other lineages. nature.com/articles/s4158… 1/16
The LSHTM team has been analysing B.1.1.7 for signs of increased or decreased severity since late December. We first identified a signal of higher mortality in mid-January. This led to an announcement by the PM and @uksciencechief on 22 January. bbc.co.uk/news/health-55… 2/16
In that early report, we estimated that B.1.1.7 was associated with a ~35% increase in mortality, based on around 2600 deaths, of which 384 had the SGTF marker for B.1.1.7. Our updated analysis is based on 4900 deaths, around 3100 of which had SGTF. 3/16
Our paper “Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England” has now been published in Science (early release: science.sciencemag.org/content/early/…). I’ve tweeted about this a few times before, so I’m going to focus here on some key messages. (1/8)
B.1.1.7 has a 43–90% higher reproduction number than previous SARS-CoV-2 strains. This holds for several different methods we used to analyse its spread, and we found similar rates of increase in the UK, Denmark, Switzerland, and the United States. (2/8)
Back in December, we predicted that B.1.1.7 would cause a huge surge in cases and that without stringent measures and faster vaccine deployment, more people in England would likely die from COVID-19 in the first half of 2021 than in all of 2020. (3/8)
We've updated our preprint on the transmissibility of SARS-CoV-2 VOC 202012/01, aka B.1.1.7, with new statistical and modelling methods. Headline: we estimate VOC is 43–82% more transmissible than preexisting variants. UNDER PEER REVIEW cmmid.github.io/topics/covid19… (1/6)
We now include new statistical estimates of B.1.1.7 growth, which accord with our earlier model-based estimates—and provide some really interesting plots. (thanks @Alex_Washburne, @inschool4life, @TWenseleers, @seabbs and @sbfnk!) UNDER PEER REVIEW (2/6)
The estimates differ slightly, reflecting the different methods used. But they all identify a significant increase in transmissibility. Of particular note, we found similar growth rates in Denmark. See also, Belgium:
@i_petersen Thanks Irene. See image, sorry for bad labelling! Essentially the major pattern is that it doesn't seem to have spread into 80+ quite as quickly. Over November, 0-19s were slightly overrepresented but that seems to have somewhat settled out now. (1/2)
@i_petersen UK scientists originally interpreted this as the variant spreading (slightly) more easily among children than preexisting variants. But with newer data now in, this may have just been a transient effect related to schools being open during the November lockdown. 2/2
@i_petersen I tried to fit way too much into one tweet here. Let me be a bit of a nerd and expand massively on this. First, by UK scientists I mean the scientists on SPI-M who I have been talking to about this, obviously I don't know what the general "UK scientist view" is. a/
I can present a brief update to our analyses of VOC 202012/01 from last week. VOC 202012/01 continues to spread in England, as shown in both sequencing data from COG-UK and Pillar 2 testing data provided by Public Health England. NOT PEER REVIEWED 1/7
While the sequencing data above are definitively VOC 202012/01, S-gene target failure (SGTF) is also associated with some other lineages. However, PHE estimates some 98% of SGTF are now VOC 202012/01 (assets.publishing.service.gov.uk/government/upl…). NOT PEER REVIEWED 2/7
Fitting a purely statistical model (logistic growth with a false positive rate representing non-VOC SGTF), we find that the spread of SGTF is consistent with a single increased growth rate for VOC 202012/01 across all NHS regions (grey ribbons). NOT PEER REVIEWED 3/7