1) We recently published a serosurvey in Nature Communications that nicely describes the development of anti-SARS-CoV-2 antibody titers in the New York City population.

nature.com/articles/s4146… 2) This was a very nice collaboration between Harm van Bakel's lab, Mia Sordillo, @VivianaSimonLab and @AubreeGordonPhD , spearheaded by @abramwagner and of course first author Juan Manuel Carreño who is leading my serology core.

1) I am reviewing some of the literature re antigenic distances between XBB.1.5 nd JN.1 and how well the XBB.1.5 vaccine works right now. I'll post random papers here. Just for nerds. (this is not a story, just a bunch of papers). 2) Interesting paper from Qatar re protection of infection from JN.1 reinfection. Take home message is probably that JN.1 is antigenically distant from XBB.1.5. medrxiv.org/content/10.110…

1) Our preprint describing 3 years of our PARIS study is live. There are a few interesting observations I wanted to highlight. This was the work of a large team but the lead is really @VivianaSimonLab medrxiv.org/content/10.110… 2) First, here is an overview of the spike titers of all the study time points. We had 501 individuals in the study and measure their anti-spike binding antibodies on a regular basis.

1) I feel this paper by Mattias Forsell's group is often overlooked but shows something very important: Binding antibody to SARS-CoV-2 spike - in the absence of strong neutralizing antibodies to a new variant - predict protection from mortality. .thelancet.com/journals/lanep… 2) Individuals with the lowest antibody titer have the highest risk, individuals with higher titers are protected. Of course, we are not talking about protection from infection or protection from symptomatic disease by binding, non-neutralizing antibodies here, but protection....

1) In a recent study with @gabagagan, Anass Abbad, Juan Manuel Carreño and @VivianaSimonLab we wanted to see how much crossreactivity exists in the post-COVID era to spikes beyond SARS-CoV-2. We expressed all the spikes shown in the tree below and got going. 2) We ran ELISAs with longitudinal samples from people who had received the primary vaccination series of COVID-19 mRNA vaccines including naive individuals (grey) and people who previously had SARS-CoV-2 infections (black).

1) I just talked with students in class about similar situations in France and Spain in the last few years. Aedes mosquitos are present in the US and Europe and are a nice vector for dengue. Once the virus is established in local mosquito populations its hard to get rid off.

https://twitter.com/pucksandviruses/status/1636416463253782561

2) And climate change helps the mosquitos to move north, extending the potential range for viruses like dengue, chikungunya, Zika etc. This is also happening for some tick species, e.g. Hyalomma ticks in Europe which can carry Crimean-Congo Hemorrhagic Fever Virus.

1) What should be done about avian influenza. Very easy. Master seed viruses and vaccines specific to the panzootic H5N1 need to be produced (which is likely in progress for a some time already, the CDC is really good at this and BARDA has manufacturing contracts for it). 2) It needs to be assess if these viruses are sensitive to the three classes of drugs we have against influenza. To my knowledge that has been done, looking good. There is likely also significant immunity to the N1 because humans have been exposed to pH1N1 which...

1) Why do I get so worked up about e.g. the new NIH data sharing policy or other bureaucracy that is piling up on PIs? Most of these things are useful and are implemented with good intentions. But our days are full, many of us are burned out (especially those involved... 2)....in the pandemic response) and every little bit of additional work adds to that. A new piece of bureaucracy that is now required may mean I have to work a few hours more on a weekend. Or it may mean that I can't do sports this week. Or, it may mean....

1) Here is a little story about the new data policy from NIH. It is 5:34am and I am already upset and my blood pressure is high. We wanted to do everything right. We got a paper accepted in @JVirology and worked diligently with @niaidcivics SDMCC to get all the data in the.... 2)...paper submitted to @ImmPortDB which is one of the data repositories that are ideal for our kind of immunology data. The idea was that when the paper goes online, it already has an ImmPort identifier so that people who want the data can just....

My friendly neighbour gave me a booklet which was provided to UK and US soldiers who went to Austria after WWII as a short intro to the country. Its an amazing read (thanks Andy!!!). It also contains this gem. The last sentence explains a lot of the current problems. More gems. Do's and don'ts:

1) Boston University researches have made a SARS-CoV-2 virus that has the spike of Omicron BA.1 and the remaining genome of the ancestral SARS-CoV-2. Now they got in trouble because this research was funded by the US government (NIH) but they did not ask the NIH... 2)....if they were allowed to do so. Here is an excellent overview article about the case: statnews.com/2022/10/17/bos…

1) A sad story: A physician in Austria was facing credible and horrific online death threats because she endorsed SARS-CoV-2 vaccination. She had to invest lots of money into security and in the end had to give up her office. An incompetent police force wasn't able to help. 2) Last Friday she was found dead, very likely due to suicide. derstandard.at/story/20001378…

Currently 2 hours delayed at the gate at JFK because it seems @Delta can't find a pilot. Interesting. Update: Pilot showed up and we boarded. Now we are sitting in the plane waiting for a decision if luggage from people rebooked on a second flight to the same destination should be unloaded. My connection to Stockholm is now toast.

Alright, the SAVE (SARS-CoV-2 Assessment of Viral Evolution program) paper is out!

"Defining the risk of SARS-CoV-2 variants on immune protection"

nature.com/articles/s4158… Many researchers from the US and internationally are contributing to this huge effort to early detect and quickly characterize variants. Juan Manuel Carreño in my lab and my colleagues @VivianaSimonLab, @mschotsaert, Harm van Bakel and Adolfo García-Sastre are major contributors.

1) Es gibt mittlerweile Medikamente, die, wenn sie früh genug genommen werden das Risiko eines schweren Verlaufs von COVID-19 drastisch reduzieren. Paxlovid ist eines diese Medikamente und ist in der EU zugelassen. Ziel sollte es sein, dass solche Medikament leicht zugänglich... 2)...sind. Jeder Hausarzt sollte darüber Bescheid wissen und es sollte Risikopatienten auch direkt nach einem positiven Test im frühen Stadium der Erkrankung verschrieben werden. Ich weiss nicht, wie die Versorgungslage in Österreich da grad aussieht, aber...

1) We now often hear about 'universal coronavirus vaccines' in the media. I think development of a universal coronavirus vaccine is an important goal that may be achievable in the long run if sufficient funding is available. But I think we should not make any false promises..... 2) ....about short term successes and the media should really make sure to use correct nomenclature. I'll try to explain what I mean with this with the below figure. Its a rough phylogenetic tree based on the spike protein sequences of different coronaviruses. There are four....

1) On January 25th 2023 a new data sharing policy from NIH kicks in which basically requires raw data from NIH-funded studies to be shared. Data is defined as: 2) "The recorded factual material commonly accepted in the scientific community as of sufficient quality to validate and replicate research findings, regardless of whether the data are used to support scholarly publications."

1) I am very worried about Omicron and inactivated vaccines. According to early data from the UK, 2x AstraZeneca or 2x Pfizer provides little protection from symptomatic disease. VE with inactivated vaccines is generally lower (as shown e.g. in Brazil: medrxiv.org/content/10.110…) 2) Its also unclear how other vaccines like Sputnik, Soberana-2, Cansino, Zydus Cadila's DNA vaccine etc. will hold up. If updated vaccines are needed (which now seems likely), can this be done quickly for non-vector and non-mRNA vaccines?

1) First data from the UK seems to indicate that there is little protection from Omicron for people vaccinated twice, but the booster dose seems to be 75% effective against symptomatic disease. Early days, wide confidence intervals. This looks likely better for severe disease. 2) Here some links to the data: khub.net/documents/1359… and assets.publishing.service.gov.uk/government/upl….

1) What do I think about Omicron now that some neutralization data is available? My impression hasn't change. We seem to see a drastic reduction in neutralizing activity, far more than with previous variants. Little activity was left in vaccinated individuals and it is likely.... 2)....that very little activity is left in convalescent individuals. However, people who were infected and then vaccinated did have residual neutralizing activity despite a drastic reduction. This certainly also bodes well for vaccinated individuals who received their....

1) My gut feeling from hearing of Omicron cases in Botswana, ex-Malawi, ex-Egypt (2 now it seems) and in South Africa is, that the variant was flying under the radar in undersequenced countries for some time until Botswana and South Africa detected it and sounded the alarm. 2) However, the fact that European countries only detected it in travelers after South Africa and others warned about it, probably means that many cases so far went undetected. It also tells us a lot about genomic surveillance in some high income countries.