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Dr Kevin Purcell ๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ‡ฎ๐Ÿ‡ช๐Ÿ‡บ๐Ÿ‡ธ ๐Ÿ˜ท๐Ÿ’‰ Profile picture
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22 Feb, 6 tweets, 2 min read
A random takeaway: a lot more old (> 65 years old) people are getting AZ vaccine rather than Pfizer in the UK.

Especially very old people ๐Ÿคทโ€โ™‚๏ธ

The โ€œyoungโ€ tail, I presume, is healthcare workers.

An interesting test of efficacy in older people?

Preprint:

drive.google.com/file/d/162PJKbโ€ฆ
For more on the Scottish study of people receiving both AZ and PB vaccines (initially mentioned in the Daily Mail, go figure) see this thread:

Also the slightly odd y axis in the preprint caused Theo to replot the graph with linear axes (probably better for Daily Mail readers who understand hazard ratios!).
The original plot is:
Or in tabular form:
And a direct (non-Google Drive) copy of the pre-print

โ€œEffectiveness of first dose of COVID-19 vaccines against hospital admissions in Scotland: national prospective cohort study of 5.4 million peopleโ€

Dr Eleftheria Vasileiou PhD, Usher Institute

ed.ac.uk/files/atoms/fiโ€ฆ

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Dr Kevin Purcell ๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ‡ฎ๐Ÿ‡ช๐Ÿ‡บ๐Ÿ‡ธ ๐Ÿ˜ท๐Ÿ’‰ Profile picture

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Dr Kevin Purcell ๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ‡ฎ๐Ÿ‡ช๐Ÿ‡บ๐Ÿ‡ธ ๐Ÿ˜ท๐Ÿ’‰ Profile picture
7 Aug 20
An interesting and carefully done piece of work on looking for SARS-CoV-2 in the air on a hospital patients room.

The found live virus, sequenced it and showed it was the same as the one the patient had.

There are a few caveats though. medrxiv.org/content/10.110โ€ฆ
This was done in a hospital room with at least 1 sick patient.

If the patient was emitting aerosols was that by normal respiration/speaking or by coughing?

Is the aersol from a resuspension of virus emitted as drops or droplets?
This is an n=1 study.

What was the viral load of the patient? They just report a positive PCR test not a Ct value.

Where was he emitting virus from? URT? LRT?

Is this typical of hospital patients (or any other patients)?
Read 6 tweets
Dr Kevin Purcell ๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ‡ฎ๐Ÿ‡ช๐Ÿ‡บ๐Ÿ‡ธ ๐Ÿ˜ท๐Ÿ’‰ Profile picture
23 Jul 20
โ€œSARS-CoV-2 testing and contact-tracing data from the Indian states of Tamil Nadu and Andhra Pradesh reveal stark contrasts from epidemics affecting high-income countries, with 92.1% of cases and 59.7% of deaths occurring among individuals <65yo.โ€ medrxiv.org/content/10.110โ€ฆ
โ€œThe per-contact risk of infection is 9.0% (95% confidence interval: 7.5-10.5%) in the household and 2.6% (1.6-3.9%) in the community.โ€
โ€œSuperspreading plays a prominent role in transmission, with 5.4% of cases accounting for 80% of infected contacts.โ€
Read 13 tweets
Dr Kevin Purcell ๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ‡ฎ๐Ÿ‡ช๐Ÿ‡บ๐Ÿ‡ธ ๐Ÿ˜ท๐Ÿ’‰ Profile picture
18 Jul 20
Vaccine Efficacy Needed for a COVID-19 Coronavirus Vaccine to Prevent or Stop an Epidemic as the Sole Intervention

Or โ€œHow good does a vaccine have to be to get us โ€˜Back to Normalโ€™?โ€ ajpmonline.org/article/S0749-โ€ฆ
4 pairs of plots of reduction in cases vs vaccine efficiency.

Each pair of plots for two different values of R0 (2.5 and 3.5) for a fraction of the population already immune to the disease (0%, 5%, 15% and 30%).

The lines on a plot are the fractions of the population vaccinated Image
Simulation experiments revealed that to prevent an epidemic (reduce the peak by >99%), the vaccine efficacy has to be at least 60% when vaccination coverage is 100% (reproduction number [R0]=2.5โ€“3.5).
Read 7 tweets
Dr Kevin Purcell ๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ‡ฎ๐Ÿ‡ช๐Ÿ‡บ๐Ÿ‡ธ ๐Ÿ˜ท๐Ÿ’‰ Profile picture
13 Jun 20
โ€œIn total, New Zealand has reported 1,504 confirmed and probable cases of COVID-19, including 22 total deaths. The vast majority of these (69%) were linked to travel, either in travelers who recently arrived from affected areas or contacts of travelers.โ€ outbreakobservatory.org/outbreakthursdโ€ฆ
โ€œOver the course of its epidemic, New Zealandโ€™s daily test positivityโ€”an important metric for gauging whether a country is testing enough for the size of its epidemicโ€”averaged less than 1%, which is much lower than many other countries.โ€
This worked because early on:

The stopped non-residents from entering New Zealand from infected areas.

They required residents and citizens coming from infected areas to do mandatory quarantine.

Implied: They had low travel volume (being disconnected helps).
Read 9 tweets
Dr Kevin Purcell ๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ‡ฎ๐Ÿ‡ช๐Ÿ‡บ๐Ÿ‡ธ ๐Ÿ˜ท๐Ÿ’‰ Profile picture
6 Jun 20
โ€œour results identify ZAP as an effector of the IFN response against SARS-CoV-2, although this pandemic pathogen may be preadapted to the low CpG [dinucleotide] environment in humans.โ€

And no, it doesnโ€™t mean taking lots of zinc will cure COVID. biorxiv.org/content/10.110โ€ฆ
Not CpG dinucleotides (5'โ€”Cโ€”phosphateโ€”Gโ€”3' , that is, cytosine and guanine separated by only one phosphate group) are used in regulation of gene expression by methylation of the cytosine.

CpG sites are underrepresented in the human genome.

en.m.wikipedia.org/wiki/CpG_site
*Note (not not).
Read 11 tweets
Dr Kevin Purcell ๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ‡ฎ๐Ÿ‡ช๐Ÿ‡บ๐Ÿ‡ธ ๐Ÿ˜ท๐Ÿ’‰ Profile picture
5 Jun 20
Interesting study from Vietnam.

โ€œAsymptomatic SARS-CoV-2 infection is common [43%] and can be detected by analysis of saliva or NTS. NTS viral loads fall faster in asymptomatic individuals, but they appear able to transmit the virus to others.โ€ academic.oup.com/cid/advance-arโ€ฆ
14,000 tested for SARS-CoV-2

49 were positive.

But only 30 participated in the study (chance for selection bias?)

13 (43%) never had symptoms and 17(57%) were symptomatic.

17 (57%) participants acquired their infection outside Vietnam (travels more likley to be selected?).
THey donโ€™t put error bars on the asymptotic fraction.

An estimate for the standard deviation of the asymptomatic result (from Poisson stats) is 30% to 55% (and even wider than that if you want 95% CI 20%-65%).

Interesting but it doesnโ€™t nail it down!
Read 11 tweets

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