Interesting paper from colleagues in China, studying evolution of omicron in great detail. They find evidence for antigenic seniority, ie preferential boost of responses to original antigens encountered. In breakthrough in vaccinees, that is Wuhan wild type virus.
They select B cells binding to RBD, then sequenced Ig coding genes, then expressing these as monoclonals and test for neuts against a range of mutants to map the specific antibodies to a set of previously defined epitopes targeted by neutralising and non neutralising antibodies.
They show that breakthroughs of BA2, BA5 preferentially induce non neutralising antibodies and map the specific antibodies to a set of previously defined epitopes targeted by neutralising and non neutralising antibodies
They then go ahead to predict further escape mutations, and test those in pseudoviruses, showing that a handful of them can lead to full “ plasma escape” (note again: coronavac vaccinated)
They warn that this eventually may lead to complete escape variants with possibly more severe disease association as a concern, though there is evidence for the latter. They also conclude that broad spectrum vaccines will be needed
In all, a beautiful piece of work , technically challenging, and showing some in depth analysis of observations that had been done before. I do however think we need to be a bit carefull extrapolating this globally.
Important caveat: the paper does not describe any of the sample backgrounds: timing of vaccination, of infection, of boosters and of sampling in relation to all of these. That can make all the difference in the world. Questions: would you observe the same in a later time point?
Another caveat when interpreting the vaccination response: this was coronavac, in a few individuals. Known to induce comparatively low levels of neutralizing antibodies so less likely cross reactive neutralising antibodies.
I do wonder about “unprecedented accelerated evolution”. Is evolutionary rate omicron unusual, and/ or is it the scale of circulation that makes this visible. Sparking of lineages is not unique for omicron. We also saw that for delta
in all, nice work, through provoking, but caution to extrapolate too widely.
Correction: there is NO evidence

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More from @MarionKoopmans

Sep 16
De kamerbrief over lange termijn aanpak COVID19. Veel informatie rijksoverheid.nl/documenten/kam… Met name de uitleg over hoe VWS de aanpak ziet: indicatie COVID19 thermometer dor response team, advies sectorplannen via maatregelenladder. Zie voorbeeld Image
een dergelijk plan is per sector opgesteld, maar er zijn behoorlijke overeenkomsten. Ook wel opmerkelijke verschillen. Bijvoorbeeld preventief testen niet in elk sector plan onder preventie.
uitleg over het maatschappelijk impact team dat in April was aangekondigd. Volgens de brief gaat het in september starten. Als viroloog vind ik dat erg laat. Cijfers beginnen nu op te lopen. Geen paniek, maar die maanden in de zomer waren toch handig geweest om MIT te starten
Read 6 tweets
Sep 15
Ok, here it is, the report of the lancet commission on SARS COV 2, led by Jeff Sachs. The chair is an expert specialized in economics and has worked at high political level. covid19commission.org/jeffrey-sachs
I look at the part that I consider my expertise: understanding and responding from a virology and public health perspective. You can stop reading here if you consider me conflicted because I am a virologist involved in a cover up. If you are interested, proceed
commission description: “ the Lancet editors work with academic partners to identify the most pressing issues in science, medicine, and global health, with the aim of providing recommendations that change health policy or improve practice”. thelancet.com/lancet/commiss…
Read 20 tweets
Jun 12
viral RNA persistence is not restricted to sites classically considered immune privileged, but can also occur in other sites including blood, lymphoid tissue, joints, respira- tory tract, gastrointestinal tissues, and kidney, with a variety of known and unknown consequences Image
Review summarising evidence of viral RNA persistence for a range of infections, and the possible consequences of those observations when discussing COVID 19. Ebola and Marburg filovirus, Zika virus, measles virus as examples.
Persistence often not in primary sites of infection but in sites where immune response is less effective OR in cells that are part of the immune system. Virus culture may be negative, but evidence for intact full length genomes is used to argue active replication.
Read 5 tweets
May 20
OMG there is all these DISEASES..... This is what i am hearing a lot. Due to COVID, the world is more aware, and outbreak reports that have been there throughout now all of a sudden get noticed. Yes, there is (new) disease outbreaks every day. See eg promedmail.org
Or this resource healthmap.org/en/O (I use to for teaching). All of this is based on what individuals share, as part of global intelligence. There is a whole army of experts behind it, assessing the signals, studying them, doing research.
This has been a very much neglected part of science. And right now, you may say, investments are coming? Not too optimistic: what I see is money for vaccines, diagnostics, far less for the board " intelligence" agenda. But we should be pushing for that.
Read 6 tweets
May 19
The outbreak of monkeypox is starting to be worrisome. We have seen occasional imported cases, usually dead ending. In this situation, new cases have been detected in different countries. That is very unusual.
Monkeypox as we know it is not that contagious. Question therefore is: was anything special happening explaining this situation? A very unusual index with many direct contacts for instance? Or is there something unusual about the virus?
Could that have become more transmissible. The old cousin to monkeypox, smallpox, used to be much more contagious ( and virulent). What exactly determines that is not clear but it is know that genome deletions can be a way by which these viruses evolve.
Read 4 tweets
Apr 6
paper out of my area of expertise, author's intro: the government of a country with an individualistic culture can be more hesitant in initiating restrictions which may compromise personal freedom; nature.com/articles/s4159… a synopsis
"at the social level, citizens of country with an individualistic culture are less likely to follow government orders, rendering social distancing, mobility restrictions and other government-initiated policies more difficult to enforce".
"In sum, while an individualistic culture has its indisputable merits, they can potentially thwart an effective fight against COVID-19 due to the difficulty in both policy coordination and social uncooperativeness, resulting in a less effective containment of the pandemic".
Read 6 tweets

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