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A Marm Kilpatrick Profile picture
A Marm Kilpatrick
@DiseaseEcology
Disease Ecology, Population Biology
Adam Smithee Profile picture Timothy McDonnell Profile picture Rulito Profile picture NLW Profile picture wyomingnan Profile picture 9 subscribed
Oct 29, 2022 • 14 tweets • 5 min read
How to mislead in science: hide raw data in supp material (SM).
Just had a dept-wide reading group of a recent Science paper on latitudinal/temperature trends in predation pressure (10.1126/science.abc4916). Paper claims simple clean patterns (fig) but where are the data??? Panel A (L) in main text. Raw data & regional analysis in SM. Paper makes simplistic & general claim: predation increases w/ Temp. But data tell v different story. Instead of clear increase in Bait Consumption w/ Temp, pattern is absent in 2/4 region, strong in 1/4, weak in 1/4.
Jun 23, 2022 • 5 tweets • 3 min read
COVID-19 vs Shark attack
There was a shark attack yesterday where I free dive frequently (abc7news.com/lovers-point-b…). A friend asked what's more dangerous, COVID-19 or swimming/free diving with sharks in the ocean?
Just for fun, here's a rough calculation.
tl;dr COVID-19 by a mile. Chance of COVID-19 infection? Depends on many things: occupation, household size, behavior, exposure of household members etc. But in US roughly 60% of US has been exposed in last 2 years (webmd.com/lung/news/2022…). So crude estimate of yearly chance of infection 37%.
May 2, 2022 • 5 tweets • 2 min read
Why would Amazon workers vote against union & why aren't union dues progressive like taxes (i.e. lowest for lowest income)?
I've read several stories (nytimes.com/2022/05/02/tec…) about workers at 2nd Staten Island plant voting strongly against union but none of the articles say why. Union dues would be $5/week for full time employees (amazonlaborunion.org), so if earning $15/hr, this is 0.33 hrs/week or 0.8% of salary which seems pretty cheap, & is even less than some large unions (e.g. Teamsters = 2.5 hr/mo or ~0.55hr/wk).
Apr 19, 2022 • 15 tweets • 5 min read
Florida Manatees: doomed to extinction or actually doing pretty well?
A simple data analysis story.
Some of you may have seen this article in NYTimes 10d ago:
nytimes.com/2022/04/09/us/… The article suggests Florida manatees are on their way out with quotes like this:
Feb 8, 2022 • 4 tweets • 2 min read
#epitwitter
Need help w/ UK seroprevalence data
I recall previously seeing estimates of for SARS-CoV-2 infection for UK, but now I can only find estimates for exposure to spike protein which is infection OR vaccination (fig from
ons.gov.uk/peoplepopulati…)
but... I want seroprevalence for infection so need data on antibodies to nucleocapsid protein or other non-spike protein. Does this exist?
Feb 3, 2022 • 7 tweets • 3 min read
US COVID-19 deaths US >2000/day & continue to rise.
I can't help but wonder if focus on Omicron's mildness contributed to size of surge & deaths occurring now.
Difference in severity was small relative to higher infectiousness. Latter should have been singular focus of messaging. Obviously it would have been far worse if omicron had been as severe as Delta. But focus on mildness of Omicron by scientists, media, government, CDC, etc. contributed to people being less safe than they should have & now thousands are dying/day & many more w/ long covid
Jan 20, 2022 • 5 tweets • 2 min read
What is an "acceptable" # of COVID-19 deaths in US?
Lots of folks suggesting that post-omicron we can pretend we're post-pandemic.
But 1K deaths/d = 365K deaths/yr
Flu avg is ~35K/yr
We need avg ~100deaths/day to get near flu
We've never had daily avg <225 since Mar 2020 We'll need deaths to plummet post-Omicron & stay low (no new variants - wishful thinking!) to get even close. Otherwise we'll need higher vaccination coverage or other ways to keep transmission lower.
Or accept much higher deaths as "normal". Good to be explicit if that's it.
Dec 22, 2021 • 6 tweets • 3 min read
Fundamental misunderstanding of what it means for Omicron to result in less severe illness. Still no studies compare hospitalization in naive people infected w/ Omicron & Delta. All studies simply measure effect of vaccination + previous infection which we know reduce severity. Here's best attempt to control for vaccination status & prev infection (including undetected cases). It finds 0-30% reduction in risk of hospitalization. That's tiny & much smaller than other studies that don't account for this.
imperial.ac.uk/media/imperial…
(cont)
Dec 8, 2021 • 35 tweets • 18 min read
How effective are vaccines against Omicron?
Today 3 studies were posted of data on immune escape measured by reductions in "antibody neutralization titers".
We can use these to estimate VE, WITH SOME ASSUMPTIONS.
Thread based on paper w @billy_gardner_ that we'll post tomorrow We've known since the discovery of Omicron's growth & posting of it's sequence that it has many mutations in its spike protein, & many of these affect binding of our antibodies. @jbloom_lab estimated that these would reduce binding of antibodies 20-60 fold:
Nov 29, 2021 • 9 tweets • 2 min read
How much faster can we detect Omicron by sequencing more cases?

As many countries try to determine if Omicron is present, one simple approach is to sequence more. How much time does this buy us? A simple calc puts things in perspective.
tl;dr sequencing 5x more buys ~13-40d The math:
The probability of detecting something by sequencing N samples given it is present at a prevalence P is simply:
1-(1-P)^N
Graphically, this relationship for two lowish prevalence values is:
Nov 27, 2021 • 13 tweets • 5 min read
Observations on new variant detected in Africa (Omicron)
-Many countries have closed borders, but I haven't heard of any that are simultaneously sending 10M vaccine doses to Africa.
-Closing borders while R>1 locally is silly. Virus is likely already widespread at v low freq. -w/ no data, it's a bit shocking to see reputable people promoting 1 doctor's anecdotal observations that Omicron causes mild illness. If claim was opposite the same (always optimistic) scientist would demand to see data & suggest we don't believe it w/out rigorous analyses.
Nov 24, 2021 • 6 tweets • 3 min read
How do we get broad immunity to SARS-CoV-2 that will protect against future variants?
2 studies (are there more?) suggest that vaccination followed by infection gives broader protection than infection followed by vaccination.
@florian_krammer @profshanecrotty @GuptaR_lab 1st paper (medrxiv.org/content/10.110…) shows: if you get vaccinated w/ mRNA vaccine & have a breakthrough Delta infection your subsequent antibodies are almost equally reactive in neutralizing Delta, Beta, Alpha, WT.
Oct 27, 2021 • 26 tweets • 15 min read
Should we all get a vaccine booster (3rd dose)?
New preprint w @billy_gardner_ , we examine impact of 3rd doses on key topic: transmission.
medrxiv.org/content/10.110…
tl;dr 3rd dose could significantly reduce Rt & stop some surges, but doses should 1st go to unvaccinated if possible Background
COVID-19 vaccines are fantastic. Better than we could have imagined. mRNA vaccines had efficacy of ~95% for symptomatic disease & even better for severe disease & death. But there's now strong evidence that protection against mild disease & infection is waning a bit.
Sep 10, 2021 • 16 tweets • 5 min read
What is driving current peaks in SARS-CoV-2 cases & what does this mean for the fall & winter?
Although a peak might seem to indicate that we're headed for fewer cases until a new variant arises, unfortunately that's not the case & a surge is both likely & avoidable.
A thread. One possibility is in nice thread @trvrb suggesting US Delta surge is peaking now b/c 5% more of US pop infected, driving Rt down to 1 (which occurs at peak).
Jun 15, 2021 • 4 tweets • 1 min read
Nice thread @EdMHill describing modeling from 1 of 3 teams on possible outcomes in UK that guided recent decision to postpone re-opening.
Big takeaways:
-I wish US gov had been open to scientific guidance in 2020
-Big uncertainty in behavior changes w/ re-opening
cont. -Big uncertainty in relative transmissibility of delta (b.1.617.2) variant & vaccine effectiveness for transmission (not symptomatic disease). PHE-UK has provided fantastic real-time analyses of available data, but some critical data, that could be collected, are missing.
May 26, 2021 • 9 tweets • 5 min read
Why hasn't B.1.1.7 fully displaced other variants in US? What other variants are persisting/growing?
Thread
B.1.1.7 has risen to relatively high frequencies in many states, but hasn't exceeded 90% in any of them & may be falling in several.
Data here from @my_helix GISAID sequences via fantastic outbreak.info for US as a whole suggest B.1.1.7 now stable @70%, P.1 is growing, B.1.526 frequencies are stable. But variable sequencing means finer resolution is better for understanding frequency dynamics, spatial variability & nuance.
May 26, 2021 • 7 tweets • 3 min read
Yesterday I posted the tweet below as a joke.
Today I found so much bullshit (@callin_bull) it blows my mind.
Exhibit 1: The press release itself: investors.modernatx.com/news-releases/…
Yup, they claim 0 vs 4 cases = 100% efficacy.
Exhibit 2: NBC, USA today both parrot 100% efficacy claim. Exhibit 3: Moderna CEO claims vaccine prevents infection (see quote). Note: there was no data presented from study on efficacy against infection (despite that being #1 reason to vaccinate kids). Only symptomatic disease (4 cases total), antibody response, & side effects.
May 22, 2021 • 25 tweets • 11 min read
What is the trajectory of viral load dynamics & test sensitivity post-INFECTION?

We're 17 month into the pandemic &, shockingly, this Q is still only partly answered.
Recent paper using a study design I proposed 12 months ago provides detailed look & raises many questions. Background
We know that ~3-6d following infection COVID-19 symptoms start (the incubation period). doi:10.1136/
bmjopen-2020-039652
May 21, 2021 • 17 tweets • 9 min read
How effective are vaccines vs severe & all disease, death, infection, & transmission?
Very nice collection of studies assessing different aspects of vaccine protection by Julia Shapiro (on twitter?) @nataliexdean @betzhallo @ilongini & 2 others.
Thread
medrxiv.org/content/10.110… Study has data on many different measures of protection:
all infection (symp + asymp), all symptomatic (mild+severe), severe, hospitalization, death, & transmission,
for 8 vaccines: Moderna, Pfizer, Novavax, Astrazeneca, Sinopharm, Sinovac, Sputnik, J&J,
3 variants&
1&2 doses
May 20, 2021 • 11 tweets • 5 min read
Should vaccinated people stop wearing masks?
Happy to contribute to article @B_resnick w @MonicaGandhi9 @AbraarKaran @DocJeffD @DrJeanneM
Short thread w/ my perspective on how to navigate CDC guidance on masks post-vaccination.

vox.com/science-and-he… 1st: Protection from vaccination is NOT 100% (no surprise to anyone that follows me to hear this)
So, despite being vaccinated, I'm still going to wear a mask in what I consider high(er) risk situations - indoors w/ dozens of households, unless community transmission is VERY low.
May 4, 2021 • 6 tweets • 2 min read
Interesting thread @trvrb on growth of B.1.1.7, P.1, B.1.351 in US
I worry about key assumptions underlying these analyses:
-sequences are random sample of state/US infections (definitely not)
-trends in sequences represent local transmission rather than changes in imported cases Many of the P.1, B.1.351 numbers are very low & introduced cases can make a substantial contribution to total count. Increased transmission elsewhere (e.g. Europe, S America) & constant introductions can lead to apparent increase in US for foreign variants.