Thread by @BallouxFrancois

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.
academic.oup.com/ooim/article/3…
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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.
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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.
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outbreak.info

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.
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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.
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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.
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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.
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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.
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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).
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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.
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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)
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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.
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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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