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The BA.4 & BA.5 Omicron subvariant-driven increase of new confirmed Covid cases in South Africa gives a good idea of what the endemic equilibrium will look like: a significant wave every 6 months with significant mortality & morbidity. 
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Here the different variant waves shown with weekday effects smoothed out & with a correction for variable testing intensity applied...
And also a plot of estimated true number of infections by variant through time, using the @IHME_UW estimates of true infections per day (including undiagnosed ones). This shows what a massive infection wave Omicron BA.1+BA.2 caused...
Here shown in terms of cumulative numbers, as a % of the population. According to these estimates, the true number of infections now exceeds the South African population size. So much for that fantastic mucosal immunity.
The cumulative # of infections that the UK saw, per the @ONS infection survey results, may be roughly similar. But there is one major difference: a decent vaccine rollout & uptake greatly reduced Covid mortality compared to SA, where only 30% are fully vaccinated & 4% boostered.
In SA, the Omicron BA.1+BA.2 wave still cost 25 000 excess deaths, ca. 2.5 x that of seasonal influenza there. Globally, the Omicron wave still caused an estimated 3 million excess deaths, ca. 6x as many that die from influenza each year. https://www.economist.com/graphic-detail/coronavirus-excess-deaths-estimates">https://www.economist.com/graphic-d...
But with Covid likely to cause 2 waves per year. In SA, newly diagnosed cases now double week on week & cases are rising in all provinces. To soon to know what impact will be on hosps & mortality, but hosps are rising in KwaZulu Natal & Gauteng Province. https://twitter.com/rid1tweets/status/1518627955995463686">https://twitter.com/rid1tweet...
This rise in cases is a little faster than expected based on the growth rate advantage of BA.4 & BA.5 per se (logistic growth advantage of 0.12 per day [0.09-0.15] 95% CLs compared to BA.2). Maybe waning immunity or behavioural or seasonal change also contribute.
![This rise in cases is a little faster than expected based on the growth rate advantage of BA.4 & BA.5 per se (logistic growth advantage of 0.12 per day [0.09-0.15] 95% CLs compared to BA.2). Maybe waning immunity or behavioural or seasonal change also contribute.](https://pbs.twimg.com/media/FRNdwxLXIAETTm5.png "This rise in cases is a little faster than expected based on the growth rate advantage of BA.4 & BA.5 per se (logistic growth advantage of 0.12 per day [0.09-0.15] 95% CLs compared to BA.2). Maybe waning immunity or behavioural or seasonal change also contribute.")
The growth rate advantage of BA.4 & BA.5 over BA.2 is similar than that of BA.2 over BA.1 and of Delta over Alpha. But with caveat that BA.4 & BA.5 carry 2 mutations in the spike receptor binding domain that are predicted to confer some immune escape. https://twitter.com/jbloom_lab/status/1513537998314356736">https://twitter.com/jbloom_la...
The mutations in question, L452R and F486V, were previously selected against, but now have an advantage in a population with high Omicron BA.1 immunity. And hence, will now cause a wave of reinfections.
I hope that medicine agencies and pharmaceutical companies still manage to up the pace at which adapted vaccines can be made available. At Pfizer the production time for an adapted vaccine is now reduced to 21 days, so that is not the bottleneck - the regulatory side is...
It& #39;s as if medicine agencies still haven& #39;t come to terms with the fact that SARS-CoV2 evolves ca 2.5x faster than the fastest evolving influenza strain. And that vaccine updates would have to be made twice as fast then as for influenza... https://twitter.com/trvrb/status/1511871593940545536">https://twitter.com/trvrb/sta...
Mind you - also for influenza, vaccine effectieveness would be a lot better if adapted vaccines could be developed in less than 6 months. Right now VE against infection with the influenza virus ranges between 10% and 60%.
Mistakes in predicting which strain will dominate so long in advance is the main cause of poor performance. E.g. this year it was just 16%. https://www.idse.net/Respiratory-Tract-Infections--Influenza/Article/04-22/Flu-Vaccine-Match-Not-the-Best-This-Season/66750?utm_source=Social&utm_medium=twitter&utm_campaign=0414mat">https://www.idse.net/Respirato...
