@RolandBakerIII I don't think this paper suggests people were exposed to #SARSCoV2 20 years ago. Rather, it suggests that at a very low frequency some human antibody gene rearrangements will bind strongly to the #SARSCoV2 RBD even in the absence of an immune response selecting for this. (1/n)
@RolandBakerIII This is not terribly surprising. For instance, it's known that even naive humans sometimes have a bit of antibody reactivity to the #SARSCoV2 RBD (see Fig 1B of this paper by @SCOTTeHENSLEY). Indeed, this type of rare low-level naive reactivity...
@RolandBakerIII @SCOTTeHENSLEY is the basis for an immune response, which must start with some binding.

Additionally, these antibodies have genes similar to IGHV3-53, which is known to naturally bind well to the RBD with minimal somatic hypermutation. (3/n)
@RolandBakerIII @SCOTTeHENSLEY Finally, note that the experiments in onlinelibrary.wiley.com/doi/10.1002/ad… involve three rounds of phage panning. Mutations can arise during the phage propagation and selection, so this could serve as a directed evolution process to further increase antibody affinity. (4/n)
@RolandBakerIII @SCOTTeHENSLEY (Sorry, here is paper referenced in above Tweet: sciencedirect.com/science/articl…)

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More from @jbloom_lab

14 Oct
In a new study led by @AllieGreaney, we show that infection with a #SARSCoV2 variant elicits an antibody response with somewhat shifted specificity relative to early Wuhan-Hu-1-like viruses that were circulating early in the pandemic: biorxiv.org/content/10.110… (1/n)
It's now known that #SARSCoV2 variants have mutations that reduce neutralization by antibodies elicited by early viruses, which are source of spike in current vaccines. This figure from @VirusesImmunity shows neutralization drops for common variants: (2/n)
But do the antibodies elicited by infection with these variants have different specificities, such that humoral immunity from infection with variants will be differentially affected by specific mutations? (3/n)
Read 14 tweets
7 Oct
To answer below question, most bat CoV don't bind human ACE2 strongly, but can happen incidentally in evolution. Presumably because some mutations that increase binding to bat ACE2s incidentally increase binding to human ACE2, which has substantial homology to bat ACE2s. (1/6)
One example is recently described BANAL-20-52 bat CoV, which binds human ACE2 strongly (researchsquare.com/article/rs-871…). Another is SHC014 (ncbi.nlm.nih.gov/pmc/articles/P…), which @TheMenacheryLab @Baric_Lab showed infects human cells despite having evolved in bats. (2/6)
More broadly, we recently did large yeast-display survey of SARS-related CoV RBDs and found that some bind human ACE2 (and some ACE2s from other species) well despite being from bats (biorxiv.org/content/10.110…). (3/6)
Read 6 tweets
21 Sep
For anyone who doesn't want to do alignments, here are spike amino-acid mutations separating #SARSCoV2 from newly discovered bat CoV BANAL-20-52, which is #SARSCoV2's closest known relative in spike.

Mutations as #SARSCoV2 Wuhan-Hu-1 to BANAL-20-52 in #SARSCoV2 numbering. (1/6)
There are 16 amino-acid substitutions across the 1273-residue spike.

In addition, there is an indel at the furin cleavage site, since like all other known bat sarbecoviruses, BANAL-20-52 lacks the furin cleavage site found in #SARSCoV2. (2/6)
For comparison, Beta and Delta #SARSCoV2 variants each have 7 amino-acid substitutions relative to Wuhan-Hu-1.

So BANAL-20-52 spike about twice as diverged as current #SARSCoV2 variants are from early #SARSCoV2, *plus* of course BANAL-20-52 lacks the furin cleavage site (3/6)
Read 7 tweets
13 Sep
This is a really good and thoughtful thread by @stuartjdneil! It's great to see these clear explanations and chains of reasoning that more and more virologists are posting about the topic of risk-benefit of certain experiments. (1/3)
I had posted some of my own thoughts here (), and other virologists like @wanderer_jasnah @stgoldst have made excellent points in various comments and replies. (2/3)
It's clear we all agree that most virology experiments are valuable & safe with current biosafety rules.

Then there is a small slice of experiments that most agree are too risky.

Finally, there is a gray area that requires nuanced weighing of risks and benefits. (3/4)
Read 4 tweets
11 Sep
Hi @angie_rasmussen, thanks for asking these important questions about risk / benefits of different types of virology experiments. Because you locked your Tweet thread, I can't reply, so will post my thoughts here in a new thread that anyone can reply to. 🧵
This is not about being pro- or anti-chimeric virus, but about risks of specific experiments. As scientists we have this responsibility. My favorite essay is Feynman's The Value of Science (calteches.library.caltech.edu/40/2/Science.p…), which he wrote after his field of physics built nuclear bomb.
As we all know, experiments that manipulate viruses have yielded important scientific insights & been of tremendous value to human health. This includes smallpox vaccine, oncolytic viruses, gene delivery, etc. Even some vaccines (eg, J&J #SARSCoV2 vaccine) are chimeric viruses!
Read 23 tweets
1 Sep
@zeynep, here are some more interesting early #SARSCov2 dates for you. Check out the description of the samples in the final published version of this paper (academic.oup.com/cid/article/71…): "Eight COVID-19 pneumonia samples were collected from hospitals in Wuhan in January 2020." (1/3)
See if you can spot difference in how same samples are described in PubMed Central version (ncbi.nlm.nih.gov/pmc/articles/P…), which would have been built from original peer-reviewed manuscript: "Eight COVID-19 were collected from hospitals in Wuhan from December 18 to 29, 2019." (2/3)
Journal early access version of manuscript, which would have been the peer-reviewed version, also says samples from December 18-29, 2019 (web.archive.org/web/2020030800…). There is no correction in journal, so presumably dates changed at post-peer review manuscript proofing stage. (3/3)
Read 7 tweets

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