Now out with @rebeccajk13 Interpreting vaccine efficacy trial results for infection and transmission…
funded in part by #SeroNet
In which we show that earlier work by Rinta-Kokko et al on interpreting prevalence measures for vaccine efficacy generalizes to the COVID-19 case and that the odds ratio for PCR+ in vax vs unvax persons swabbed at random
is under reasonable assumptions a lower bound on the vaccine's effect against transmission, the critical quantity for herd immunity that combines reduced risk of acquiring and shorter duration.
We further show that combined vaccine effect #VE measures using symptomatic + a proportion of asymptomatic cases have no clear interpretation, and swabs of _only_ asymptomatic don't either. Thus random x-section regardless of symptoms is the way to go.
Alternatively, testing the contacts of known cases can estimate VE against acquisition (VES in the parlance of @betzhallo @ilongini & C Struchiner), conditioned on infection, an approach taken in… with @G_RegevY et al., in press in @LancetRH_Europe
As an example we take the data from the @moderna_tx vaccine RCT. Among asymptomatic persons at the second vaccine visit, the odds of PCR+ were 61% lower among vaccine recipients than placebo recipients. By the approach we advocate, this indicates one dose of Moderna vax
reduces one's ability to transmit the virus by >= 61%. We suggest it is probably considerably greater than 61% (apart from the statistical uncertainty in this estimate, which is substantial given small numbers) for 3 reasons.
1) only asymptomatics were swabbed, which tends to underestimate protection vs. swabbing all individuals; 2) a few individuals might have been infected before the vaccine was yet effective, and still shedding at the time of dose 2 (likely small effect);
3) doesn't account for any vaccine effect on the amount of shedding, which other studies show is substantial and likely further reduces transmission risk.
Much more work needed to quantify transmission effects but this is good news, esp. for one dose.
Next preprint in this line of work looks at viral shedding as an outcome… with @LeeKShaffer joining @rebeccajk13 and me -- still under peer review

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More from @mlipsitch

25 May…. A key point: lab leak does not imply manipulation and manipulation does not imply ill intent.
I disagree with @SenTomCotton on many many things but this set of tweets quoted in the article lays it out correctly
In contrast this statement is illogical “However, since we observed all notable SARS-CoV-2 features, including the optimized RBD and polybasic cleavage site, in related coronaviruses in nature, we do not believe that any type of laboratory-based scenario is plausible.”
Read 4 tweets
13 May
This tweet got me thinking again about a topic that's been on my mind for the last several weeks and throughout the pandemic. In principle I fully agree with @flodebarre that people should evaluate arguments for logical soundness and consistency with facts, not who makes them.
But many people have asked me (most recently @AmyDMarcus) how thoughtful people should know whom to trust in getting information (science) and advice (for personal actions) and opinions (about policy) on a topic like COVID
Consistent with @flodebarre's tweet, my first response was you shouldn't trust anyone intrinsically, but should trust good arguments. As a scientist, that is how we are (or should be, there is still too much hero worship in our field) trained.
Read 28 tweets
13 May
In this clip @SenRandPaul FALSELY claims… that the @cambridgeWG has characterized work at the Wuhan Institute of Virology as gain-of-function.
I and many other @cambridgeWG support proper investigation of SARS-CoV-2 origins including the lab leak hypothesis and continue to oppose many forms of GOF research but it is just fabrication to say we have made any statement as a group about work in Wuhan.
What we called for was a moratorium on GOF research until proper risk-benefit calculations can be done. Just as this pandemic was starting, two of us were strongly critical of how @NIH and @HHSGov evaluate GOF proposals…, calling for much more transparency.
Read 5 tweets
12 May
Really important @nytimes article on how easy access to vaccines remains a key issue not just hesitancy…. I’d add two points less explicit in article
1. People say that seeing others get vax without incident reduces their hesitancy. If so then each vaccine administered to those where access is the main problem can have a multiplier effect in overcoming hesitancy in others.
2. If we think of getting vaccinated like any other choice then hesitancy and ease of obtaining are two sides of same coin. If hard to get, a little hesitancy will stop. If easy to get, only the very hesitant won’t.
Read 4 tweets
30 Apr
Great that attention is remaining focused on #AMR a big problem.… . But the relentless claims that this is primarily or largely a problem of agriculture are not evidence-based.
Some years ago @BillHanage and I and @G_RegevY and our students pointed out the absence of strong evidence (while acknowledging challenges of generating it)…
Recent excellent genomic work from Prof Sharon Peacock's group, @MarcBonten's group among others has failed to find evidence of strong links between resistance in animals and resistance in clinical isolates. @BillHanage wrote about this…
Read 4 tweets
19 Apr
Is there some bizarre legal notion of causality at play here that the force used would have had to be such that it would have killed anyone, not just the actual person it did kill?
I'm willing to believe that the law traditionally has such a notion (or not -- hope some lawyers will help me understand) but if so it seems truly indefensible. We all have the preexisting condition of being mortal. We each have a different breakpoint for how much...
of a certain kind of abuse we can survive. It seems incoherent to have a standard that it's not murder if a different person would not have died under the same horrific abuse -- and I'm not saying that is true, only that this seems to be the defense's standard.
Read 4 tweets

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