In a new study, I identify and recover a deleted set of #SARSCoV2 sequences that provide additional information about viruses from the early Wuhan outbreak: biorxiv.org/content/10.110… (1/n)
Bloom Lab
3,914 posts
Bloom Lab
@jbloom_lab
Lab studying evolution of proteins and viruses. Affiliated with @fredhutch @HHMINEWS @uwgenome.
Opinions are my own and do not reflect those of my employer.
- I wanted to summarize what is known about the new XBB.1.5 variant of SARS-CoV-2, which is starting to generate a lot of interest. (There are no new scientific results in this thread, it simply aggregates previously reported results for those not following topic closely.)
- Here's how mutations in #SARSCoV2 Nu variant (B.1.1.529) will affect polyclonal and monoclonal antibodies targeting RBD. These assessments based on deep-mutational scanning experiments; underlying data can be explored interactively at jbloomlab.github.io/SARS2_RBD_Ab_e… (1/n)
- We mapped how all mutations to #SARSCoV2 receptor-binding domain (RBD) affect recognition by convalescent polyclonal human sera (biorxiv.org/content/10.110…). Among implications: E484K (South African lineage) worrying for immune escape; RBD mutations in UK lineage less so (1/n).
- Replying to @jbloom_labFinally, my analysis is on GitHub at github.com/jbloom/SARS-Co… where you can access all code, data, & paper drafts. All updates are via time-stamped commits. This ensures transparency/reproducibility of this study are not in doubt, regardless of your views on interpretation. (25/n)
- In new study, I have analyzed correlation between SARS-CoV-2 & animal genetic material in full set of environmental samples from Huanan Seafood Market. biorxiv.org/content/10.110… Analysis clarifies what sequencing these samples can & cannot tell us about early outbreak at market.
- Replying to @jbloom_labThere are also broader implications. First, fact this dataset was deleted should make us skeptical that all other relevant early Wuhan sequences have been shared. We already know many labs in China ordered to destroy early samples: scmp.com/news/china/soc… (16/n)
- In new work, we show a human coronavirus evolves to escape neutralization by antibody immunity (biorxiv.org/content/10.110…). Specifically, we studied the historical evolution of the common-cold CoV-229E to learn how #SARSCoV2 might evolve & if we might need to update vaccines. (1/n)
- I wanted to summarize current knowledge about origins of the #SARSCoV2 Omicron variant. (This 🧵 doesn’t have anything new for people following topic closely, but I still get many questions about this, so am recapping current knowledge.)
- In letter published in @ScienceMagazine today, I join 17 other scientists in calling for further investigation of #SARSCoV2 origins, including objective consideration of both accidental lab leak and natural zoonosis: science.sciencemag.org/lookup/doi/10.… (1/n)
- Replying to @jbloom_labReason people are discussing XBB.1.5 is because it’s so transmissible. Below are estimates of current Rt (measure of transmissibility) of different variants in US from @trvrb’s group. XBB.1.5 more transmissible than other variants like BQ.1.1 that until recently dominated in US
- Replying to @jbloom_labWe should therefore avoid dogmatic arguments about #SARSCoV2 origins / early spread, and instead focus on following two questions: (1) How can we get more data? (2) How can we better analyze the data we have? (24/n)
- We've written a perspective on a new study by @MAMdayIndayOut that helps explain why some viruses (measles) don't evolve to escape immunity but others (influenza) do. Provides some clues relevant to future for #SARSCoV2 as well: cell.com/cell-reports-m… Here is a recap: (1/n)
- Replying to @jbloom_labBoth progenitors suggest #SARSCoV2 was circulating in Wuhan before December outbreak at Huanan Seafood Market, which is corroborated by lots of other evidence, including news articles from China in early 2020 (see intro to my paper linked in first Tweet in this thread). (15/n)
