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KATarinambraun's profile
Katarina Braun
Katarina Braun
Katarina Braun
@KATarinambraun

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Katarina Braun

@KATarinambraun

PhD ‘21 from @tcflab at @UWMadison. Current M4 & aspiring #obgyn physician-scientist @UWMSTP. Interested in viral evol'n esp in context of pregnancy. She/her.

Madison, WI
github.com/katarinabraun
Joined September 2015

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    Katarina Braun‏ @KATarinambraun 30 Apr 2021

    New preprint 📢 We deep seq’d #SARSCoV2 and found within-host diversity is limited and rarely transmitted & transmission bottlenecks are narrow → slows the pace of #VOC emergence in *acute* infxs. We need to 👀 carefully at long-term infxs. 🧵 1/12 ⬇️https://go.wisc.edu/dlm7zd 

    7:00 PM - 30 Apr 2021
    • 85 Retweets
    • 254 Likes
    • Z Prediction CCLabRat Crash Richmond Gavin Zhang,PhD @ABclonal_USA Laeeth Andrei Papkou Alex Merz felix
    6 replies 85 retweets 254 likes
      1. New conversation
      2. Katarina Braun‏ @KATarinambraun 30 Apr 2021

        This was a highly collaborative project. 🙏 Many thanks to @wcassias, @KatiaKoelle, @dho, @trvrb, and @tcfriedrich. Incredible leadership and mentorship from start to finish on this project from @LouiseHMoncla. And, of course, my partner in crime/science, @GageKMoreno. 2/12

        1 reply 1 retweet 14 likes
        Show this thread
      3. Katarina Braun‏ @KATarinambraun 30 Apr 2021

        The emergence of #SARSCoV2 VOCs is concerning and raises❓s about vaccine updates. Growing evidence says VOCs might arise during long-term infxs, but the vast majority of infxs are acute. So, we asked: can novel variants arise + transmit efficiently in acutely infected ppl? 3/12

        1 reply 3 retweets 14 likes
        Show this thread
      4. Katarina Braun‏ @KATarinambraun 30 Apr 2021

        To answer this❓, we deep seq’d viruses from 133 #SARSCoV2 genomes and 28 putative household transmission pairs, and take advantage of our large consensus-level surveillance dataset (n=5,517) from the community where these individuals reside. 4/12

        1 reply 1 retweet 13 likes
        Show this thread
      5. Katarina Braun‏ @KATarinambraun 30 Apr 2021

        Genetic diversity within hosts was very limited. Most of the infxs we looked at had ≤5 iSNVs, the majority of which were low frequency. Most iSNVs can only be found once and the variation that was shared was homopolymers and Wuhan-1 reversions. 5/12pic.twitter.com/JSXWmTt4rn

        1 reply 3 retweets 16 likes
        Show this thread
      6. Katarina Braun‏ @KATarinambraun 30 Apr 2021

        Half of all putative household transmission pairs (14/28) share no iSNVs at all. A quarter of these pairs (7/28, purple) share more iSNVs than expected by chance (chance = random pairs, grey). Not enough shared variation to infer transmission w/o epi data. 6/11pic.twitter.com/LXSKygUnLs

        1 reply 2 retweets 13 likes
        Show this thread
      7. Katarina Braun‏ @KATarinambraun 30 Apr 2021

        We found a *single* instance of a within-host iSNV arising later at consensus levels. Even w/ a relatively dense dataset, we find NO evidence of iSNVs commonly giving rise to consensus SNPs along phylogenetically linked infxs. iSNVs in *acute* infxs ≠ consensus diversity. 7/12

        1 reply 1 retweet 12 likes
        Show this thread
      8. Katarina Braun‏ @KATarinambraun 30 Apr 2021

        Transmission bottlenecks in household pairs are *narrow* and sensitive to the variant calling threshold. Narrow bottlenecks → diversity is lost at the time of transmission → limited shared diversity in households and in phylogenetically linked infxs! 8/12pic.twitter.com/5nzeWykE1J

        2 replies 2 retweets 17 likes
        Show this thread
      9. Katarina Braun‏ @KATarinambraun 30 Apr 2021

        Results of #SARSCoV2 within-host studies have varied a bit. We think it’s in part bc #SARSCoV2 is particularly vulnerable to method error. Our study emphasizes the importance of duplicate sequencing for any studies relying on low-freq iSNVs to infer biological processes. 9/12pic.twitter.com/pAxIL8jKZS

        1 reply 1 retweet 16 likes
        Show this thread
      10. Katarina Braun‏ @KATarinambraun 30 Apr 2021

        Overall, our data suggest acute infxs are unlikely to be common sources of novel variants. Future work is needed in long-term infxs / immunocompromised hosts where there is more time for mutations to arise, selection to act, and transmission to occur. 10/12

        1 reply 9 retweets 27 likes
        Show this thread
      11. Katarina Braun‏ @KATarinambraun 30 Apr 2021

        Check out these other great #SARSCoV2 within-host studies from @katrina_lythgoe and @alvalesano: 11/12 https://science.sciencemag.org/content/372/6539/eabg0821 …https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009499 …

        1 reply 2 retweets 14 likes
        Show this thread
      12. Katarina Braun‏ @KATarinambraun 30 Apr 2021

        Check out these #SARSCoV2 studies looking at evolution in chronic infxs: 12/12 https://www.nejm.org/doi/full/10.1056/NEJMc2031364 … https://academic.oup.com/jid/article/223/1/23/5934826 …https://www.nature.com/articles/s41586-021-03291-y …

        1 reply 1 retweet 11 likes
        Show this thread
      13. Katarina Braun‏ @KATarinambraun 30 Apr 2021

        BONUS. One of our favorite parts of working on a new manuscript is getting to choose a new color scheme. This paper’s color scheme was inspired by the amazing women of the 2021 inauguration. 💃https://github.com/ciannabp/inauguration …

        4 replies 2 retweets 44 likes
        Show this thread
      14. End of conversation

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