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… 1/
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. 3/ 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. 5/
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. 8/
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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The situation in Gaza is horrific, and if anything its is getting worse by the day, but the estimates of ~400,000 deaths that have been circulating recently are not plausible. 1/
The origin of this number is a (mis-)reading of an excellent piece of analysis that used IDF data (link in the thread below). 2/
Importantly, the study did not estimate death tolls. By summing up the number of people in the three 'safe zones' provided in the figures, one gets ~1.85M, a shortfall of ~400k people in Gaza relative to Oct 7. After accounting for the ~100k people who left Gaza, this might suggest ~300k deaths.
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Bombing hospitals is a war crime. It can never be justified because there were soldiers / militants being treated or because local doctors are (high-ranking) officers, which is standard practice in many countries.
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Whether military / mixed facilities are located nearby or even within / underneath, again a common practice in many countries, does not make hospitals fair targets. Even bombing military hospitals is a war crime.
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Following the recent strike by Iran on the Soroka hospital in Beersheba, it looks like hospital bombings is getting some attention. Though it is far too common and occurrence is increasing globally.
Map of the 5 Israeli/American/GHF “aid distribution” compounds in Gaza. The compound's locations doesn't overlap with the displaced civilian population, at all, likely intentionally so. 1/
The same map with the distance in miles to the closest compound. Weakened, sick people, kids or the elderly can hardly walk such distances in scorching heat in a barren landscape. 2/
This is a set-up for one of the compounds. It may be an understatement that it hasn't been designed primarily to maximise the comfort and well-being of the population. 3/
H5N1 bird flu has a mortality rate close to 100% in chicken. When the virus is detected in a chicken farm, all animals are being euthanised to reduce their suffering and limit the risk of spread to other animals and humans. 1/
Culling all the chicken in a farm where H5N1 is circulating is the correct response, epidemiologically, ethically and morally, and it is standard procedure globally.
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Elon Musk has just become the ultimate outrage disinformation machine. Whenever I see a tweet by him on any topic I know something about, he's totally, utterly wrong.
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This is a brilliant - if technical and terse - reanalysis of the modelling that led to the double spillover claims for SARS-CoV-2. I feel it is fair to say that it puts to rest, once for all, the previous evidence published in favour of a multiple spillover scenario. 1/
That said, in the grand scheme of things, it actually doesn't matter that much - besides correcting the scientific record.
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I actually find it intriguing that so much energy has been wasted on this fight, since the number of spillover events of SARS-CoV-2 lineages (two mutations apart) does not constitute a strong argument in favour, or against, any scenario for the origin of SARS-CoV-2.
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Children sniped 2.
[There was a bizarre disinformation campaign against this article - the NYT stood by their reporting] 2/ nytimes.com/interactive/20…