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DiseaseEcology's profile
A Marm Kilpatrick
A Marm Kilpatrick
A Marm Kilpatrick
@DiseaseEcology

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A Marm Kilpatrick

@DiseaseEcology

Disease Ecology, Population Biology

Univ California Santa Cruz
kilpatrick.eeb.ucsc.edu
Joined August 2013

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    1. A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

      Here's a graph illustrating possibilities. We know from meta-analysis @nicolamlow that 20% of infections are asymptomatic https://doi.org/10.1371/journal.pmed.1003346 … (see 1.placebo group). If vaccine only reduced disease but not infections, we'd get option 2 - no reduction in total infection but...pic.twitter.com/Sf40qLpi9Q

      3 replies 6 retweets 95 likes
      Show this thread
    2. A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

      a 95% reduction in symptomatic infections but a huge INCREASE in asymptomatic infections. If vaccination reduced both symptomatic & asymptomatic infections 95% we get outcome 3. Finally, it's possible to get outcome b/w 2 & 3, shown as outcome 4.pic.twitter.com/LwOz6mMu0k

      2 replies 11 retweets 80 likes
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    3. A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

      A Marm Kilpatrick Retweeted A Marm Kilpatrick

      What do the data indicate? A *CRUCIAL* bit of data was shared from Moderna trial based on swabs taken on day of 2nd dose. These data showed a 61.5% reduction in infections on this day. But was this estimate of reduction in total infections or asymptomatic?https://twitter.com/DiseaseEcology/status/1339093206122655747 …

      A Marm Kilpatrick added,

      A Marm Kilpatrick @DiseaseEcology
      Moderna (in supplemental doc: https://www.fda.gov/media/144453/download …): Tests on swabs from date of 2nd dose showed ~2/3 lower PCR+ in asymptomatic people. No stats done; but pretty strong effect (simple binomial prop: P=0.0012). pic.twitter.com/qHVyNzSY7O
      Show this thread
      2 replies 11 retweets 73 likes
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    4. A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

      The difference is *crucial*. If reduction is in total infections, then it's better than outcome 2, but only 2/3 of the way towards outcome 3. If reduction is in asymptomatic infections then much better b/c w already know symptomatic infections are 95% lower.

      1 reply 5 retweets 67 likes
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    5. A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

      I emailed authors of study (DOI: 10.1056/NEJMoa2035389) & Dr. El Sahly was kindly able to confirm that the swabs represent truly asymptomatic infections. This is fantastic because it indicates we have outcome 4 - reductions of 95% in symp. & 61.5% in asymp infections.pic.twitter.com/Nkfe5ehi0y

      6 replies 42 retweets 207 likes
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    6. A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

      Finally, a very recent paper from @RoyKishony Israel suggested that infections following vaccination reduces viral load by ~2 Ct starting 12d after 1st dose (https://doi.org/10.1101/2021.02.06.21251283 …)pic.twitter.com/Y1ZgJXPEGy

      3 replies 22 retweets 122 likes
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    7. A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

      Another recent set of papers showed that lower viral loads are strongly correlated with lower transmission https://twitter.com/DiseaseEcology/status/1357117171369824258 …pic.twitter.com/0XXqi8z0rs

      2 replies 24 retweets 146 likes
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    8. A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

      Linking these last two datasets is a little tricky given diffs in Ct b/w labs & logistic relationship b/w Ct & transmission- I've done a back of the envelope version below. Also vaccine from Israel study is Pfizer, not Moderna. This only affects transmission efficacy calculation.

      1 reply 4 retweets 64 likes
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    9. A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

      If we put this all together, I *think* we can estimate the (minimum) reduction in both infection & transmission from vaccinated individuals. *Minimum* b/c reduction in asymptomatic infections & viral load is based on data BEFORE 2nd dose. Efficacy should improve w/ 2nd dose.

      3 replies 11 retweets 102 likes
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    10. A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

      Point estimate: Infection efficacy: (IE) 0.8*0.95+0.2*0.385=88.3% Transmission efficacy: IE*0.93^2 (.93 per log, 2 logs) = 89.9%

      9 replies 8 retweets 86 likes
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      A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

      Incorporating uncertainty from each component (except Ct-infectiousness correlation) w/ parametric boostrapping produces median reductions of 90% (87-93%) in infection & 91% (89-94%) of transmission (Note: many CIs were not symmetrical so median !=mean/point estimates):pic.twitter.com/4enSxpQvdK

      10:53 AM - 9 Feb 2021
      • 20 Retweets
      • 118 Likes
      • Holly Quick Michael Flohr a.k.a. Níthilhêr The Colourless Gwen Brandt MD eys M Marks Herbie Lewis Laura Ehrig 🌎💙 grrpaige.eth Bazaari, show coal some ❤️
      2 replies 20 retweets 118 likes
        1. New conversation
        2. A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

          Note that infection reduction calcs are based on Moderna vaccine (no data on asymp infection for Pfizer). As noted above, trans reduction calcs use data from Pfizer, so a little bit of mixing & matching which is less than idea, but vaccines are very similar so prob not far off.

          6 replies 8 retweets 70 likes
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        3. A Marm Kilpatrick‏ @DiseaseEcology 9 Feb 2021

          Have I made an error somewhere? If so, please let me know and I'll revise & update. (or if it's a big error, I'll delete the whole thread). @mlipsitch @nataliexdean @JoannaMasel @LucaFerrettiEvo

          15 replies 3 retweets 86 likes
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        4. A Marm Kilpatrick‏ @DiseaseEcology 10 Feb 2021

          Add1: I made a couple typos (that don't change calcs but confused people; apologies) in showing calcs of point estimates: Reductions in infection should have been: 0.8*0.95+0.2*0.615=88.3% Reduction in transmission 1-[(1-0.883)*0.93^2] = 89.9%

          2 replies 1 retweet 22 likes
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        5. A Marm Kilpatrick‏ @DiseaseEcology 10 Feb 2021

          Add2: h/t @taaltree Reduction in transmission due to lower viral loads from an individual person has more uncertainty than pop estimate calc above. This expands 95% CI quite a bit so reduction for individual is: 91% (84%-96%)

          2 replies 1 retweet 22 likes
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        6. A Marm Kilpatrick‏ @DiseaseEcology 10 Feb 2021

          Add3: h/t @JamesGWood_UNSW Data from 2nd swab is point prevalence estimate, not precise measure of all asymp infections. If duration of RNA shedding differs b/w vacc & unvacc, this alters ratio of prev vs # infect. Overall effect on reduction in infection is small if... (cont)

          1 reply 1 retweet 18 likes
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        7. A Marm Kilpatrick‏ @DiseaseEcology 10 Feb 2021

          ratio of shedding durations is not huge (e.g. <2 or 1/2) b/c 95% efficacy for sympt inf is main effect & asymptomatic prev was (61.5%) lower. I thought I saw data on lower duration of shedding w/ vaccine but can't find it. @RoyKishony @segal_eran Please link to it if you can.

          5 replies 0 retweets 18 likes
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        8. A Marm Kilpatrick‏ @DiseaseEcology 11 Feb 2021

          Add4: @mlipsitch Some of the PCR+ swabs @ 2nd dose will be detecting RNA from infections that occurred before vaccine has any efficacy. If we use 12d post-1st dose as cutoff, then if incidence ~constant, using @bennyborremans we can estimate this as... https://elifesciences.org/articles/60122 pic.twitter.com/iTjyu2mkPs

          1 reply 0 retweets 7 likes
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        9. A Marm Kilpatrick‏ @DiseaseEcology 11 Feb 2021

          Frac of cases days 1:12 of 1:28=12/28 Prob of detecting RNA from these cases (simple linear interpol.): 0.255 Swabs + in vaccine group on day of dose 2= 15 12/28*0.255*15=1.64 swabs still being detected by residual RNA from cases detected on days 1-12

          1 reply 0 retweets 5 likes
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        10. A Marm Kilpatrick‏ @DiseaseEcology 11 Feb 2021

          Add5: Vaccine efficacy in reducing infection (incidence) can be calculated (w/ assumptions) using point prevalence P using eq from doi:10.1016/j.vaccine.2009.04.009 (h/t @mlipsitch) But, 1-P_V & 1-P_C =~1, b/c P_V=15/14,711 P_C=39/14,617 so correction (1-P_C)/(1-P_V)=0.998pic.twitter.com/kIY9Ugn3TZ

          1 reply 0 retweets 7 likes
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        11. A Marm Kilpatrick‏ @DiseaseEcology 11 Feb 2021

          Accounting for two revisions above increases efficacy estimates a tiny bit, but it's lost in rounding estimates to avoid over-precision: Infection: 90% (86%-93%) Transmission: 91% (82%-96%) New boxplot w/ more draws to show full range of outcomes.pic.twitter.com/RSTqYSrGtX

          2 replies 4 retweets 33 likes
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        12. A Marm Kilpatrick‏ @DiseaseEcology 15 Feb 2021

          Add6 Reduction in viral load following vaccination (see above) didn't indicate if infections were symptomatic. If all were symp., then reduction in loads for symp. & asymp. infections w/ vaccine & might be *much* larger than above & further reduce infectiousness.

          1 reply 0 retweets 16 likes
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        13. A Marm Kilpatrick‏ @DiseaseEcology 21 Feb 2021

          Add7 Calc above rests on assumption of fraction of infections that are symptomatic (80% from meta-analys). If this fraction is lower, reduction in infection is lower. At extreme (all infec asymptomatic) reduction in fraction infected is 61.5%. Here's a simple fig showing this:pic.twitter.com/wS1gJnkHwc

          2 replies 1 retweet 7 likes
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        14. A Marm Kilpatrick‏ @DiseaseEcology 26 Feb 2021

          A Marm Kilpatrick Retweeted A Marm Kilpatrick

          Update: Vaccination reducing asymptomatic & total infections 2 new studies provide real-world estimates to assess calculations above Caveat: both are observational studies 1st paper, reduction in all infections: 21d post dose1: 72%; 7d post 2nd dose, 86%https://twitter.com/DiseaseEcology/status/1363947185973325826 …

          A Marm Kilpatrick added,

          A Marm Kilpatrick @DiseaseEcology
          Real-world Pfizer vaccine (& natural infection) efficacy against sars-cov-2 INFECTION New Lancet paper posted today with fantastic data. https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3790399 … Short Thread tl;dr 1 dose reduces infection 72% on day 21; 7d post 2nd dose, 86%; previous infection 90% pic.twitter.com/IRaMFicMcN
          Show this thread
          1 reply 3 retweets 6 likes
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        15. A Marm Kilpatrick‏ @DiseaseEcology 26 Feb 2021

          2nd paper: 46% reduction in asymptomatic infections comparing days 1-12d post-vaccination to 13d+ (w/ hint that viral loads also lower but N=4 far too small). Unfortunately study doesn't provide data to compare total infections between 1-12d, 13d+. https://d197for5662m48.cloudfront.net/documents/publicationstatus/58516/preprint_pdf/57fc48596954cc34c20b579f8aca0383.pdf …pic.twitter.com/NddOemLfcB

          1 reply 1 retweet 4 likes
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        16. A Marm Kilpatrick‏ @DiseaseEcology 26 Feb 2021

          Data from 3rd paper (but NOT against all infections; just symptomatic & a fraction of asymptomatic) indicates that vaccine efficacy increases from d14-21 so comparisons grouping 1-12d, vs 13-24 underestimate efficacy. DOI: 10.1056/NEJMoa2101765pic.twitter.com/3sVGy5PKCF

          1 reply 1 retweet 6 likes
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        17. A Marm Kilpatrick‏ @DiseaseEcology 26 Feb 2021

          Together these studies provide independent evidence for vaccines reducing total infections (not just symptomatic infections). None are directly comparable to calculations above (differences: day of comparison, Pfizer vs Moderna, observational vs RCT) but they suggest...

          1 reply 1 retweet 9 likes
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        18. A Marm Kilpatrick‏ @DiseaseEcology 26 Feb 2021

          -Reductions in total infections from 1st paper (https://twitter.com/DiseaseEcology/status/1363947185973325826 …) are likely lower than my initial calcs (w/ barely overlapping CIs): -Pfizer, day 21 post 1st dose: 72% (58%-86%) vs -My calcs: Moderna day 28 post 1st dose: 90% (86%-93%)pic.twitter.com/9hbEsQEtha

          1 reply 1 retweet 6 likes
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        19. A Marm Kilpatrick‏ @DiseaseEcology 26 Feb 2021

          My *guess* for slight discrepancy is the estimate I used for the fraction of infections that are asymptomatic was too low (see above for how this affects calculation).

          1 reply 0 retweets 5 likes
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        20. A Marm Kilpatrick‏ @DiseaseEcology 26 Feb 2021

          Regardless, data from study #1 above shows that 7d+ after 2nd shot, efficacy against total infection is 86% (76%-97%) which, if supported by future studies, would be fantastic! (Note that none of these new studies address transmission)pic.twitter.com/CaCa1PJKcY

          2 replies 1 retweet 9 likes
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        21. A Marm Kilpatrick‏ @DiseaseEcology 28 Feb 2021

          New paper @mlipsitch on same Q: how much do vaccines reduce infection & transmission: https://www.medrxiv.org/content/10.1101/2021.02.25.21252415v1 … Paper considers Q more generally & for Moderna. Will probably write full thread later. tl;dr Estimate is essentially identical to what I suggested above 89.5% (85-93).pic.twitter.com/PbqJLBOKwp

          1 reply 4 retweets 18 likes
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        22. A Marm Kilpatrick‏ @DiseaseEcology 28 Feb 2021

          A Marm Kilpatrick Retweeted Marc Lipsitch

          @mlipsitch has written a thread on paper:https://twitter.com/mlipsitch/status/1366172405119541250 …

          A Marm Kilpatrick added,

          Marc LipsitchVerified account @mlipsitch
          New preprint on estimating and Interpreting vaccine efficacy trial results for infection and transmission | medRxiv. With ⁦@rebeccajk13⁩. Long discussion on applications to observational VE studies https://www.medrxiv.org/content/10.1101/2021.02.25.21252415v1 …
          Show this thread
          1 reply 3 retweets 9 likes
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        23. A Marm Kilpatrick‏ @DiseaseEcology 18 Mar 2021

          Another paper: data on Pfizer vaccination reducing infection. Asymptomatic pre-procedural screening suggests 79%-80% lower infection 10d post 1st dose/0d post 2nd dose. https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciab229/6167855 …pic.twitter.com/CFFhOa381y

          2 replies 4 retweets 27 likes
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        24. A Marm Kilpatrick‏ @DiseaseEcology 29 Mar 2021

          New paper suggesting mRNA vaccines reduce infection (not just disease) by 80%/90% post 1st/2nd doses in HCWs in US. Some issues w/ study design, but overall very promising. https://www.cdc.gov/mmwr/volumes/70/wr/mm7013e3.htm?s_cid=mm7013e3_w …pic.twitter.com/1CDDYCGBoj

          4 replies 7 retweets 31 likes
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        25. A Marm Kilpatrick‏ @DiseaseEcology 13 Apr 2021

          Add: 2 more papers show 1 vaccine dose lowers viral loads & thus infectiousness 20-40%. Both based on period testing (not just of sympt cases) & find larger reductions than paper above. But both are in very old pops SNF/LTCF so hard to apply to younger pop. h/t @DevanSinhapic.twitter.com/ebTeRdgGqs

          1 reply 3 retweets 18 likes
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        26. A Marm Kilpatrick‏ @DiseaseEcology 13 Apr 2021

          Studies show ~4.7 & ~7Ct differences b/w unvaccinated & single dose (Pfizer/AZ) vaccinated individuals. Using studies above these diffs likely translate to ~20-40% reductions in infectiousness for breakthrough infections. Links: https://www.medrxiv.org/content/10.1101/2021.03.26.21254391v1 …https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciab263/6188727 …

          1 reply 0 retweets 11 likes
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        27. A Marm Kilpatrick‏ @DiseaseEcology 13 Apr 2021

          I'd expect even larger reductions in viral loads w/ 2nd dose of vaccines & would love to see data from younger ages & more estimates per individual. Do these exist? Please link to them.

          2 replies 0 retweets 9 likes
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        28. A Marm Kilpatrick‏ @DiseaseEcology 26 May 2021

          A Marm Kilpatrick Retweeted Aaron Richterman, MD

          I'm adding 2 recent reviews of vaccine protection against infection, transmission, & disease: https://twitter.com/DiseaseEcology/status/1395848357461954563 …https://twitter.com/AaronRichterman/status/1395064047108829186 …

          A Marm Kilpatrick added,

          Aaron Richterman, MD @AaronRichterman
          SARS-CoV-2 vaccines substantially reduce transmission through 2 mechanisms: (1) ⬇️ chance of infection (regardless of symptoms (2) ⬇️ transmission potential of infected vaccinee Our new review of the overwhelming evidence👇🏻 @mugecevik @EricMeyerowitz https://academic.oup.com/ofid/advance-article/doi/10.1093/ofid/ofab259/6278371 …
          Show this thread
          0 replies 1 retweet 3 likes
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        29. End of conversation

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