There is a SARS-CoV-2 wave underway in many countries. Current cases are made up of a mix of Omicron BA.2.x, BA.4 and BA.5 strains. All those lineages are fairly closely related and all derive from BA.2 (pink below), which caused the previous wave.…
The BA.5 and its sister lineage BA.5.1, which differ from each other by a single pretty obscure mutation (ORF10:L37F) now account for >50% of cases in the UK. BA.2.1.12 is probably still dominant in the US at this stage.
Immunisation from reinfection stems from 'neutralising antibodies', which target particular regions of the spike (S) protein, which the virus uses to bind to host cells. All major lineages in circulation right now have a very similar S protein sequence.
As such, there is strong neutralising antibody cross-immunisation between all main lineages currently in circulation, and people who have been previously infected by BA.2 are relatively unlikely to be infected by any of the lineages in circulation now.
Protection against severe disease, death, and probably long-Covid, primarily stems from T-cell immunity. The main sites recognised by T-cells (epitopes) remain essentially unchanged across all SARS-CoV-2 lineages and variants in circulation since the start of the pandemic.
The high conservation of major T-cell epitopes across all SARS-CoV-2 variants also likely explains why vaccines despite being still based on the ancestral lineage (Wuhan-Hu-1) remain highly effective to protect against severe disease and death.
The current wave started in South Africa and then Portugal, and is over in both countries now. Portugal had a relatively severe wave likely due to the low number of prior BA.2 infections. Denmark reached peak case number, and cases are still rising in other European countries.
The BA.2.x/BA.5 wave will likely peak in 7-10 days in the UK, where it may be fairly significant (but likely well below BA.2). The situation in the US is ab bit unclear, since despite ongoing SARS-CoV-2 lineage replacement, case numbers have remained largely flat until now.
Number of cases and hospitalisations are expected to vary among countries, and will depend on a series of factors, with the proportion of previous Omicron BA.2 vs BA.1 infections likely determinant (cross-immunisation with current lineages is higher for BA.2 than BA.1).
The current wave, whilst distinct, looks largely like a rearguard action of the previous BA.2 wave in most parts of the world. Partly anecdotally, a sizeable proportion of current infections seem to be among people having dodged the virus until now.
The strains in circulation now represent various variations around BA.2, but they all seem slightly better at bypassing current host immunisation, and thus they increase in frequency. It is a bit unclear whether any of them are intrinsically more transmissible (ie. >R0)
None of the current lineages seem measurably different from BA.2 in terms of real-world tissue tropism, symptoms or virulence. So far, hospitalisation rates per case in the UK are slightly below those of the BA.2 wave, which themselves were below those of the BA.1 wave.
This wave is a pain in the neck; it would have been lovely to have a proper epi-lull over the summer, but it is a bit boring, epidemiology speaking. To compensate for the lack of drama and panic-inducing revelations in this thread, I'll give you some emojis.

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More from @BallouxFrancois

Jun 25
Large study from France on increased risk of myocarditis / pericarditis after Covid vaccination. Risk was highest during the first week after inoculation, for the 2nd dose, and for the Moderna (mRNA-1273) vaccine relative to the Pfizer (BNT162b2) one.
1/… Image
Risk for myocarditis was highest in young adults (18-24 years), but burden of both myocarditis and pericarditis across other age groups was substantial. Also both males and females seemed to be roughly equally affected.
Those data are worse than I anticipated. They don't put in doubt the overwhelmingly positive overall benefit of vaccination against Covid, but they raise questions about the merit of repeat vaccination of healthy teens, young adults, and likely also children.
Read 18 tweets
Jun 21
This preprint is getting a lot of attention. The results look indeed concerning since they suggest that re-infections are more severe than 1st infections. Though, it is not obvious that this is what the results actually show.
The study does not estimate the risk of severe disease / death following each (re-)infection. Rather it compares outcomes over a period of 180 days for people who had 1 infection vs people who had two (an infection and a re-infection).
There are some further complications, but, overall, those results do not suggest that re-infections are associated to worse outcomes on average than 1st infections.
Read 8 tweets
Jun 21
Our über-massive review on everything you always wanted to know about SARS-CoV-2, or didn't even know you wanted to know, or would have preferred not to know - but if you read it you'll know it (sorry), is out, peer-reviewed and open access.…
It's the perfect holiday read - hot pics and cool text - summarising the latest, most exciting findings on Covid, combined with a serving of arcane biology, and a smattering of obscure anecdotes that will bring chills to the back of the most seasoned Covid-doomer.
But best of all, it includes emojis, which to the best of my knowledge, is a first in the scientific literature.
Read 5 tweets
Jun 21
A number of papers have come out recently allowing to get a much better picture of the relative effectiveness of prior SARS-CoV-2 infection vs. vaccination, against risk of re-infection, symptomatic and severe disease, and death (e.g. below).
This wealth of data has also fuelled some fairly tortured arguments often focused on tidbits rather than overviews of all the available data, and at times, with a complete disregard for real-world evidence.
Such arguments range from the extent to which either prior infection and/or vaccination provide little/no immunisation, whether 'hybrid immunity' is synergistic or not, to speculations about different SARS-CoV-2 variants doing some horrible things (antigenic sin and whatnot).
Read 7 tweets
Jun 20
I got endless abuse for my vocal opposition to school closures early in the pandemic, and I still occasionally get some now. Extended school closures were widely supported by the general public, scientists and politicians.
Now that the mood has turned, we need to understand what went wrong and why, to make sure we avoid making the same mistakes again if and when the next public health crisis hits, this time making sure we put children first.
Setting up show trials singling out individuals, whose views were largely in tune with the public's anyway, won't bring solace and reconciliation. It will just prolong the climate of moral panic, mob justice and groupthink that largely led us into this mess in the first place.
Read 4 tweets
Jun 18
An interesting aspect of the pandemic has been the 'democratisation' of science. This is often viewed in a negative light and jokes about 'armchair epidemiologists' abound. Though, we may at times miss the positives of public engagement in science.
To the best of my knowledge, @KelleyKga has no background, and no formal training in epidemiology, and yet, she engages with professional scientists, robustly and competently, using logic and facts, and she gets a hearing.
I find this actually wonderful, irrespective of the exact argument. A society where the general public is involved and engaged in the science, and at times challenges professional scientists when they disagree on rational grounds, is to me a better, fairer, more equal society.
Read 4 tweets

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