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A Marm Kilpatrick Profile picture
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Feb 8 • 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?
I also can't find info on the response rate for survey. This page has response rates, but they are old (from July 2020) & they are very low (<15%). What is current response rate for serosurvey? ons.gov.uk/peoplepopulati…
Can people point me to this data if it exists?
Thank you.
@kallmemeg @JamesWard73 @SRileyIDD

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More from @DiseaseEcology

A Marm Kilpatrick Profile picture
Feb 3
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
Biggest failure, in my opinion, was lackluster efforts to roll out 3rd dose boosters, which played huge role in much smaller impact of Omicron on deaths in UK & elsewhere.
In US, many scientists argued against need for boosters, possibly b/c of global vaccine equity issues.
Read 7 tweets
A Marm Kilpatrick Profile picture
Jan 20
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.
FYI I wasn't intentionally subtweeting article by @devisridhar (saw it after posting) but obvious question is if vaccines are refused by large frac of pop, then what? I don't have easy answers but ~365K deaths/yr seems like a lot to me.
theguardian.com/commentisfree/…
Read 5 tweets
A Marm Kilpatrick Profile picture
Dec 22, 2021
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)
If you read @jburnmurdoch & @EricTopol replies you'll see that they are actually trying to answer a different question. Instead of:
1) "is Omicron intrinsically milder" they are addressing 2) "Will ratio of hospitalizations/case be lower" than for Delta wave.
Read 6 tweets
A Marm Kilpatrick Profile picture
Dec 8, 2021
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:
We measure "neutralizing antibody titers" by determining how much we can dilute a person's sera (blood) & have it still neutralize the virus & stop it from growing in cell culture. Papers often use 50% reduction in "plaques" or "foci" as a cutoff so you'll see FRNT50 as response.
Read 35 tweets
A Marm Kilpatrick Profile picture
Nov 29, 2021
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:
So, the more the better, initially ~linearly when variants are rare, but w/ diminishing returns as prevalence increases & as N samples sequenced increases.
Read 9 tweets
A Marm Kilpatrick Profile picture
Nov 27, 2021
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.
-interesting to see strong knee jerk reactions from reputable scientists (i.e. calling Omicron a scariant that we shouldn't worry about), while others take sequence data & mapping to make initial assessment that is worrisome:

Read 13 tweets

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