Marc Lipsitch

CISAC Fellowship Program

cisac.fsi.stanford.edu/content/cisa... In my new role at @stanfordcisac.bsky.social, I'm recruiting for a postdoc to define how benefits of risky research should be evaluated. w Tony Mills of @notredame.bsky.social . #philsci #biosecurity #scipolicy

Key points: A popular "hazard difference" estimator for averted outcomes is biased, but an unbiased one can be calculated from status-based aggregated data (knowing y/n vaccinated for those with and without the outcome). For avertible outcomes, this doesn't work; need to know dates of vaccination.

Defining and Estimating Outcomes Directly Averted by a Vaccination Program when Rollout Occurs Over Time During the COVID-19 pandemic, estimating the total deaths averted by vaccination has been of great public health interest. Instead of estimating total deaths averted by vaccination among both vaccinat...

New preprint reporting a large piece of work by Katherine Jia to define estimands and estimators for direct impact of vaccines with arbitrary rollout schedules arxiv.org/abs/2509.05508
with Alyssa Bilinski, @chrisboyer.bsky.social and me

Clade I mpox vaccination: strategies for deployment and evaluation Clade I mpox continues to spread in Central Africa with no sign of abating,1 however very few doses of vaccine have been deployed. Mpox vaccination strategies using either of the licenced vaccines, MV...

New paper: we argue that a promising approach for studying mpox vaccine effectiveness in Central Africa to incorporate mpox vaccination + testing data into existing cohort studies, especially those for HIV/STIs.
www.thelancet.com/journals/ebi...

There is surely some basic biology benefit to gain. But the 100s of millions spent were justified with pandemic prevention/response as part of it, and the vaccine part of that doesn't hold water.

The fact that WIV1 and HKU1 were used by Moderna doesn't mean that they were central to the science; I'm no patent expert but I guess patent applicants want to cover as many applications (eg viruses) as possible for commercial reasons. Unclear to me if using them fundamentally changed conclusions.

On the substance of your points, I am not sure about the "not dangerous because the worst viruses are already at the interface" -- depends if ecological encounter opportunities are rate-limiting, which I think we often don't know.

one argument supporting a type of research may be weak while another is stronger, or research may be both dangerous and useful (or safe and not useful) and taking points one at a time helps to keep the questions separate.

Thanks @acritschristoph.bsky.social for these thoughtful comments. Apart from space and time, one reason we didn't address the other arguments was that I think it's important to consider arguments separately to reduce pressure to form "sides" -- ...

There may be other justifications for the expense and risk incurred by such prospecting efforts, but vaccine development is not a strong one. Pathogen identification at the human interface (in spillover cases) and efforts to avoid or remediate human drivers of spillover risk may be more efficient.

For Marburg, a reservoir is known, but serious efforts at countermeasures have been spurred by human outbreaks.

We conclude that virus prospecting is neither necessary, sufficient, nor particularly feasible as a driver for medical countermeasure (at least vaccine) development.

Last, we take a look at detailed timelines of human and animal isolation of filoviruses (ebolavirus spp. and Marburg) and note that in ebolaviruses, animal reservoirs have not been confirmed but countermeasure development has followed large human outbreaks.

Then we identify the large number of targets for which vaccines are arguably more urgent than for any virus known only in non-human hosts: the 26 families of viruses known to infect humans. Among these, there are no vaccines approved for even a single member of 10 of the 26 families.

Then we note that most major virus outbreaks of the 21st century have been caused by viruses first discovered in humans. Next, we show that recent priority pathogen lists for countermeasure development have contained known human pathogens but shown little relationship to virus discovery in wildlife.

First we note that historically, finding a novel virus in animals before the first known human outbreak did not in any case spur countermeasure development. Poignant examples are Zika (1947 in animals, 1952 in humans, vaccines only much later) and monkeypox (1958-1970, vaccine R&D only recently).

In it we asked if prospecting for novel viruses in wildlife is justified, as often asserted, as a means to speeding the development of countermeasures against emerging infections. We find little evidence that it is.

What is the relationship between viral prospecting in animals and medical countermeasure development? | mBio Sampling in animal populations to detect novel viruses before they infect humans has been a major activity justified by several considerations, notably by the idea that finding such viruses will stimu...

Very pleased to share this newly published work with Aishani Aatresh, part of her exceptional Harvard undergrad thesis. journals.asm.org/doi/10.1128/... .

Good to get them <65 in advance of Medicare denying payment for progressives

Sam Harris | #425 - Are We Prepared for the Next Pandemic? Sam Harris speaks with Marc Lipsitch about pandemic preparedness.

Check out "Are We Prepared for the Next Pandemic?"- CCDD Director, @mlipsitch.bsky.social's conversation with Sam Harris, host of the Making Sense podcast. www.samharris.org/podcasts/mak...

Republicans, before you vote to close 1 of 4 nursing homes, can you update us on where those people will go?

Maybe call a few seniors in your state and go over plans for where they go next?

Or call the son whose dad has dementia and tell him how he can be a full-time caregiver?

Predicting antibody kinetics and duration of protection against SARS-CoV-2 following vaccination from sparse serological data Author summary Vaccination against SARS-CoV-2 has played a key role during the COVID-19 pandemic to lower transmission rates and reduce the number of severe cases. This is due to a vaccine-induced ris...

A new study by Julia Deichmann, @mlipsitch.bsky.social and collaborators at the Sheba Medical Center, Israel uses mathematical modeling to predict antibody kinetics and duration of protection against SARS-CoV-2 following vaccination using sparse serological data. Read it here at bit.ly/43XY9mK

Linkage-based ortholog refinement in bacterial pangenomes with CLARC Abstract. Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying g

New tool for pangenome analysis! CLARC refines bacterial gene clusters using functional annotation + linkage—not just sequence. New publication by @indragon.bsky.social & collaborators, advised by @mlipsitch.bsky.social & @billhanage.bsky.social. Read more at bit.ly/4ek0Y51

What it’s really like … to know I’m going to miss my Harvard graduation because of Trump’s travel ban Like many other international students I have had my educational dreams suspended without reason – and learned plenty about racism and resilience

Deeply affecting article by an @hsph.harvard.edu PhD student denied the opportunity to graduate due to blanket exclusion of Sierra Leone citizens by the US Government. A very particular example of pointless cruelty by the US Government. www.theguardian.com/global-devel...

There is a link for non-NIH individuals to sign in support. Already several Nobelists and others have

Bethesda Declaration — STAND UP FOR SCIENCE Support NIH Staff Now!

Remarkable open letter to the director from NIH staff on the health, financial,academic freedom, and other impacts of changes at the agency. www.standupforscience.net/bethesda-dec...

The goal is plainly and literally to cut the number of people involved in basic science in the US by 70%

Denying Visas to Chinese Students Could Backfire on America

"The policy’s narrow-mindedness will make America small again.”

I am simply at a loss to express how stupid this is.

www.nytimes.com/2025/05/30/b...

NIH cuts have doomed my research in Bangladesh — but US citizens will pay too - The Boston Globe Global partnerships have led to major scientific breakthroughs and saved millions of lives. Now, those collaborations are in jeopardy.

Great piece by @hsph.harvard.edu colleague Maitreyi Mazumdar about how NIH's evisceration of overseas research collaborations harm the US as well as the partner countries www.bostonglobe.com/2025/05/29/o...

The C.D.C. Now Says Healthy Kids Don’t Need Covid Shots. Is That True?

Thanks Dani Blum @nytimes.com for breaking down the science on kids, pregnant people, and COVID shots www.nytimes.com/2025/05/27/w...

Worth noting: we previously projected that if pregnant individuals been vaccinated at the same rate as age- and state-matched women, we would have averted 20% of maternal COVID-19 deaths (i.e., 8% of ALL maternal deaths) from March-November 2021.

doi.org/10.7326/ANNA...