Archive for SARS-COV-2

Covid-19 at NAM

Posted in Biographical, Covid-19 with tags , , on July 9, 2023 by telescoper

Public Service Announcement!

Last week’s UK National Astronomy Meeting in Cardiff was the biggest ever, and it was noticeable that very few people (less than 5%) were wearing face coverings at any point. It’s not surprising therefore that there have been reports of people testing positive for Covid-19. I don’t know how many cases have developed overall, but two people with whom I was in reasonably close contact during the conference have tested positive so, although I have no symptoms, I decided to test myself as a precaution.

Doing a test was more difficult than I thought as antigen test kits are in short supply in Maynooth these days. I tried two supermarkets and a pharmacist to no avail, and then someone in the pharmacist said she’d seen them in Aldi so I bought some there.

The result was negative:

I’ll do another one tomorrow morning just in case.

If you happened to be at NAM I’d encourage you also to get a test. If you have done one already and tested positive I’d encourage you to contact the Local Organizing Committee, who are monitoring the situation, either by email (contact details here) or via the anonymous reporting form here.

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Covid-19 in Ireland – The Last Post

Posted in Biographical, Covid-19 with tags , , , on March 1, 2023 by telescoper

On February 29th 2020, Ireland identified its first case of the novel coronavirus, SARS CoV2, the virus that causes COVID-19. The World Health Organization declared the outbreak a pandemic on March 11th. On March 12th 2020 Schools and Colleges in Ireland were closed.

Since then, I have posted regular updates of the number of cases of COVID-19, initially daily and more recently weekly as the frequency of official announcements on the data hub decreased. The plotting the latest figures actually became a sort of ritual for me over this time and I even found mildly therapeutic.

Now, however, three full years have passed- can it really be three full years? – have since the (official) arrival of the pandemic in Ireland and, with the situation looking stable, I think it’s time to stop posting these updates. I made the decision to stop at the end of February 2023 unless something drastic happened to change my mind. Ironically, I just heard this morning that one of my colleagues has a new case of Covid-19 but that hasn’t changed my mind.  I hope this makes it clear that I don’t think the pandemic is over: there are many people still suffering from new infections and the effects of “Long Covid”. I just don’t see the need to continue my updates here.

I will leave the data online here in case anyone is interested in the numbers, but I won’t be posting any further updates.

So here are the final graphs from me.  The present 7-day moving average of new cases is just 89.6 per week, down from 103.0 last week and 36 deaths were recorded in the same period.

 

On a linear scale the cases look like this

The numbers for deaths on a linear scale look like this

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A Vaccination Fallacy

Posted in Bad Statistics, Covid-19 with tags , , , , on June 27, 2021 by telescoper

I have been struck by the number of people upset by the latest analysis of SARS-Cov-2 “variants of concern” byPublic Health England. In particular it is in the report that over 40% of those dying from the so-called Delta Variant have had both vaccine jabs. I even saw some comments on social media from people saying that this proves that the vaccines are useless against this variant and as a consequence they weren’t going to bother getting their second jab.

This is dangerous nonsense and I think it stems – as much dangerous nonsense does – from a misunderstanding of basic probability which comes up in a number of situations, including the Prosecutor’s Fallacy. I’ll try to clarify it here with a bit of probability theory. The same logic as the following applies if you specify serious illness or mortality, but I’ll keep it simple by just talking about contracting Covid-19. When I write about probabilities you can think of these as proportions within the population so I’ll use the terms probability and proportion interchangeably in the following.

Denote by P[C|V] the conditional probability that a fully vaccinated person becomes ill from Covid-19. That is considerably smaller than P[C| not V] (by a factor of ten or so given the efficacy of the vaccines). Vaccines do not however deliver perfect immunity so P[C|V]≠0.

Let P[V|C] be the conditional probability of a person with Covid-19 having been fully vaccinated. Or, if you prefer, the proportion of people with Covid-19 who are fully vaccinated..

Now the first thing to point out is that these conditional probability are emphatically not equal. The probability of a female person being pregnant is not the same as the probability of a pregnant person being female.

We can find the relationship between P[C|V] and P[V|C] using the joint probability P[V,C]=P[V,C] of a person having been fully vaccinated and contracting Covid-19. This can be decomposed in two ways: P[V,C]=P[V]P[C|V]=P[C]P[V|C]=P[V,C], where P[V] is the proportion of people fully vaccinated and P[C] is the proportion of people who have contracted Covid-19. This gives P[V|C]=P[V]P[C|V]/P[C].

This result is nothing more than the famous Bayes Theorem.

Now P[C] is difficult to know exactly because of variable testing rates and other selection effects but is presumably quite small. The total number of positive tests since the pandemic began in the UK is about 5M which is less than 10% of the population. The proportion of the population fully vaccinated on the other hand is known to be about 50% in the UK. We can be pretty sure therefore that P[V]»P[C]. This in turn means that P[V|C]»P[C|V].

In words this means that there is nothing to be surprised about in the fact that the proportion of people being infected with Covid-19 is significantly larger than the probability of a vaccinated person catching Covid-19. It is expected that the majority of people catching Covid-19 in the current phase of the pandemic will have been fully vaccinated.

(As a commenter below points out, in the limit when everyone has been vaccinated 100% of the people who catch Covid-19 will have been vaccinated. The point is that the number of people getting ill and dying will be lower than in an unvaccinated population.)

The proportion of those dying of Covid-19 who have been fully vaccinated will also be high, a point also made here.

It’s difficult to be quantitatively accurate here because there are other factors involved in the risk of becoming ill with Covid-19, chiefly age. The reason this poses a problem is that in my countries vaccinations have been given preferentially to those deemed to be at high risk. Younger people are at relatively low risk of serious illness or death from Covid-19 whether or not they are vaccinated compared to older people, but the latter are also more likely to have been vaccinated. To factor this into the calculation above requires an additional piece of conditioning information. We could express this crudely in terms of a binary condition High Risk (H) or Low Risk (L) and construct P(V|L,H) etc but I don’t have the time or information to do this.

So please don’t be taken in by this fallacy. Vaccines do work. Get your second jab (or your first if you haven’t done it yet). It might save your life.

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