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The vaccine effect

Posted in Covid-19 with tags , , , on July 28, 2021 by telescoper

I saw this nifty graphic from the Financial Times floating around on social media and thought I would share it here. It’s a nice demonstration of the way the use of vaccines has impacted mortality rates from Covid-19. Basically the vaccines reduce the probability of a death by a factor greater than 10 (i.e. are more than 90% effective in doing this). On the logarithmic plot this appears as a downward shift in the “risk of death” that is more or less independent of age.

This behaviour is generally consistent with the observation that while infections in the UK are quite high the mortality rate is still rather low. Low is not zero, however, and there will still be some deaths if infection levels are high: a small fraction of a large number can still be significant.

Incidentally, about 70% of the adult population of Ireland has now been vaccinated with about 80% having received partial vaccination. The fraction of the total population fully vaccinated is about 54%. On this measure Spain has just overtaken the UK in vaccinations; Ireland is well above average for the EU. The USA and Israel have both flattened out considerably.

When I got back from my break I tried my best to update the statistics relating to Ireland here. Doing so reminded me that when I first decided to plot the data on a log y-axis I got a slew of comments on Twitter complaining that I was “manipulating the data”! The backlash against anything even simple mathematics is quite extraordinary sometimes.

Anyway, the latest logarithmic plot looks like this:

The death figures are unreliable because of the lingering effects on the ransomware attack on the Health Service Executive IT system but do seem to be much lower relative to infections than they were at earlier stages of the pandemic, even allowing for the fact that the first peak in the case curve should be higher as testing was not so extensive at this early stage. The 7-day average of new cases is currently around 1200-1300 per day.

It still fascinates me how the case numbers managed to stay roughly constant for such a long time at such a high level earlier this year…

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Per Ardua ad AstraZeneca

Posted in Covid-19 with tags , , on March 28, 2021 by telescoper

The extent to which AstraZeneca’s dishonesty concerning its purchasing agreement with the EU is becoming clearer, and the company is increasingly engulfed by a PR disaster resulting from this and misleading claims about the efficacy of its Covid-19 vaccine (see here, here, here, etc). Perhaps they will now get their finger out and actually honour their contract?

Here in Ireland there is expected to be a delivery of “large volume” of doses of the Astra Zeneca vaccine next week, though I doubt it will be as large as their contractual obligations specify. We’ll see what actually happens. There isn’t much confidence in AstraZeneca around these parts I can tell you.

This morning the Covid-19 tracker app for Ireland was updated with the latest vaccination figures for Ireland (25th March) which are as follows:

  • First doses: 548,945
  • Second doses: 211,223
  • Total: 760,168

That is definitely speeding up, which is welcome. Not as fast as the UK, of course, who have been the beneficiaries of 21 million doses exported by the EU. That’s about 2/3 of the total shots administered there. The number exported from the UK to the EU is zero. Nada. Zilch. The same is true of the USA. There’s no doubt in my mind who the bad guys are.

Anyway, not to dwell on that issue I was wondering when I might get around to having a jab myself. I am not particularly high in the pecking order, but from April onwards Ireland is supposed to receive about a million doses per month. Assuming that this actually happens, and AstraZeneca doesn’t crap out yet again, I estimate they should get to me in May (2021).

Another question that occurred to me, given that under-18s are not given the current vaccines – is how many doses are needed to vaccinate the adult population of Ireland. The total population of Ireland is about 5 million but that includes quite a large number of children. Looking at the 2016 census I see that the number of people living in Ireland who are under the age of 18 is about 1.25 million. That means to fully vaccinate the entire adult population will take about 7.5 million doses. Currently about 14.6% of the adult population have received one dose, and about 5.6% have received two. We probably won’t get to anything like full vaccination of the adult population until the autumn.

Let me just correct yet another misunderstanding often presented in the UK press concerning unused vaccines. The number of doses imported to Ireland currently exceeds the number administered by over 100,000, but that does not mean that these vaccines have been refused or wasted. Because the vaccination programme here follows the manufacturers’ guidelines, and because the supplies have been unreliable (especially from AstraZeneca), there is a buffer to ensure that a second dose will always be available on the necessary timescale for anyone who has been given the first. That means that at any time there will always be some doses in storage. It wouldn’t be necessary to do this if we could trust the delivery schedule, but there you go.

I wouldn’t be too worried about the slowish pace of vaccination were it not for the fact that new Covid-19 cases in the Republic are on the way up again:

The demographic for these new cases is quite young (a median age of 32 yesterday) and the increase almost certainly arises from lax adherence to the restrictions by a subset of the population. The relatively young age distribution and the fact that those at greatest risk of death or serious illness are being vaccinated should mean that the mortality figures remain low even as cases rise. Although the increase in new cases is worrying it is nowhere near as bad in Ireland as on the Continent of Europe and elsewhere around the world (especially Brazil). More worrying still is the likelihood of vaccine-resistant strains arising through mutation. Indeed there is already some evidence that the AstraZeneca vaccine is not as effective against the B.1.351 South African variant, although this has been disputed. Let’s hope that all the AstraZeneca doses administered so far don’t turn out to be useless.

It seems to me that it’s very likely that in order to deal with variants we’ll be having regular (perhaps annual) updated vaccine shots for the foreseeable future, as the only way to stop mutations happening is to immunize a large fraction of the world’s population and that will take a considerable time.

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The Term Ahead

Posted in Covid-19, Education, Maynooth with tags , , , , on January 28, 2021 by telescoper

After a recent Government announcement that current Covid-19 restrictions would be extended until at least March 5th, this morning we received the expected communication from the University authorities that almost all our teaching at Maynooth University would be online until March 22nd at the earliest. This is because the half-term “study break” is from 15th to 19th March (to include St Patrick’s Day) and there would be no point in trying to get students back for one week (8th-12th March) before breaking up for the following week. In fact, if I had to bet money on it I would say we’ll probably be online all the way through to the summer, and possibly beyond, but that decision has not been made yet.

To nobody’s surprise we’re also going to have online examinations in the summer again. We’ve done two rounds of these already so are getting used to them now so that’s not a problem.

The St Patrick’s Day break was basically when we flipped – by which I mean “changed teaching methods” rather than “went mad” – last year so at least we’ve already got teaching prepared for the second half of the forthcoming semester if Level 5 restrictions do continue.

I am actually a bit annoyed at the politicians for making hints about when the restrictions might end. It is clearly far too early to be talking about that. Here are yesterday’s numbers:

If you prefer them on a linear scale here they are:

New cases have fallen significantly since the latest peak but at least part of that is due to the fact that automatic close contact tracing couldn’t cope and was abandoned. Testing positivity rate has fallen to around 8.2% (from over 20%) , hospital admissions admissions are falling, and deaths may have peaked, so the evidence suggests there is a is a reduction, but the numbers are still way too high. They need to come down to much less than a 100 before any lifting of restrictions can be contemplated. At the current rate of decline that will take many weeks.  Suggesting opening up is going to happen soon will only make people impatient and reduce compliance.

Teaching term at Maynooth starts on Monday (1st February) and I have three modules to deliver, one of them a module I’ve never given before. Because there has been so much to do behind the scenes since Christmas I don’t think I’ll ever have started a term feeling so exhausted. The cycle of academic life carries on remorselessly despite the fact that everything takes longer to do under Covid-19 restrictions. It is an effort just to keep up.

Still at least we’ve all still got jobs to do and are still getting paid. It’s time to knuckle down and focus on reaching the mid-term break in one piece and then seeing where we go thereafter.

 

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Four Weeks To Go

Posted in Biographical, Covid-19, Education, Maynooth with tags , , , , , on November 23, 2020 by telescoper

As I await another Zoom meeting I remembered this cartoon from last week’s Private Eye, which sums up the prevalent mood amongst academics these days (and no doubt people in other kinds of job too).

At the start of this morning’s Panopto lecture I realised that there are still 4 weeks left of this Semester before the Christmas break. I was a bit surprised by that as this term seems to have lasted a decade already. The time certainly hasn’t zoomed by. Still, at least I’ve more-or-less kept up with my planned schedule of lectures in both of my modules without slipping. I may even be able to finish lectures to my 2nd year Vector Calculus in time to do a bit of revision in the final week.

That’s not to say other things haven’t slipped. The greatly increased time for teaching needed to move everything online hasn’t left much time for research or anything else. I keep meaning to work in the evenings to deal with outstanding things but mostly I find once I’ve done the necessary admin and teaching stuff all I can do is sleep. It seems that I’ll have to work over Christmas to finish off the backlog. Given that I didn’t have a holiday this summer that’s not ideal, but it’s unlikely I’ll be going anywhere over the “festive” season owing to Coronavirus restrictions so I might as well make the best of it.

We don’t have much idea how things will work out next Semester. The politicians seem to be wanting universities to have more on-campus teaching in the New Year. They also want to end the current restrictions to end before Christmas. In fact the current regime is suppose to end on December 2nd, which is next week, and cases are still running around 400 per day. I don’t think they can do both of these and for the Covid-19 situation to remain under any semblance of control. I think the likeliest scenario is that cases surge over the next few weeks and the Christmas break and we have to go back into full restrictions in January or February.

There is however the prospect of a vaccine or vaccines being available fairly early next year so maybe the end of this is in sight. I really hope we can get back to campus normality at some point in 2021. I do feel very sad about the effect all these restrictions has been having on the students. It’s not just having to have remote lectures. I think having a lecturer in the same room is an advantage, but the loss of it is not the worst issue. We encourage our students to work with each other in their learning, and I’m sure students learn at least as much from each other as they do from the lecturer. Peer group learning is more difficult when your peers are sitting in separate locations most of the time.

Earlier today I found myself using the phrase “getting back to normal” in connection with plans for next teaching year. Then I realise that we staff know what we mean by “normal” but our first-year students don’t. I have a feeling that may might find it more difficult to adjust to the old normal than they did to the new one.

And in any case many of our students in all years did not take up accommodation in Maynooth at the start of this year because of the remote teaching. Even if we did on campus lectures or tutorials next term, I suspect many will stay at home anyway to avoid substantial cost of rented accommodation. We will therefore have to continue making material available online whatever happens.

Anyway, what may or may not happen next Semester is to a large extent out of my hands so I won’t be making any firm decisions on what approach I will be taking until much closer to the start of Semester 2 In the meantime the goal is to fight the exhaustion and try get through to the end of term in one piece.

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Covid Questions for Ireland

Posted in Covid-19, Maynooth with tags , , on November 15, 2020 by telescoper

I’ve just done my daily update of Covid-19 numbers here and thought I’d show the latest figure:

There are now 262 data points on these graphs. When I started doing the updates I thought it might carry on for two or three months -i t’s now been almost nine and there’s no end in sight.

As you can see the 7-day average of new cases has been falling steadily since entered the period of Level 5 restrictions that is now about half-way through. That, of course, is good news. The problem is that the rate of decrease is really quite slow. The number of new cases on each day for the last week (including today) were: 270, 270, 362, 395, 482, 456, and 378 (today). That is fairly flat, the steep downward trend of the previous week apparently faltering. As a rough guess I’d say that by the time we come out of the current period of restrictions (at the beginning of December) we’ll probably still be having over a hundred new cases per day.

I think that level is far too high for comfort, but the current government is probably going to find it difficult to resist the political pressure to exit the lockdown in time for Christmas. If that does happen, I can see another lockdown looming in January. My superiors at Maynooth University are talking about having on-campus teaching again next Semester, but I think that’s highly unlikely in the circumstances.

Things are even worse in Northern Ireland where the number of new cases announced today was 478. Daily cases have been running higher there than in the Republic for some time, despite the fact that the six counties of Northern Ireland have a population of just 1.9 million compared to the 4.9 million of the 26 counties  in the Republic.

That brings me to the issue of the Pfizer Covid-19 vaccine that everyone is getting excited about. Assuming that it passes the various tests needed for it to be approved, Ireland would get about 2 million doses from the stock procured by the European Union.  The population of Ireland is about 4.9 million, and each person would require two doses, which means that supply will only enable about 20% of the population to be vaccinated.

(Actually I don’t know whether the 2 million refers to people that can be vaccinated or individual doses, but even if it’s the former that still accounts for only 40% of the population.)

The question then is who should be prioritized? I think we’d all agree that all health care workers should be vaccinated ASAP but that’s only about 25,000 people (source). Who should get the other doses? Most people seem to be assuming that those at highest risk of mortality should be vaccinated, but there’s also a case to be argued that  it should it should be those groups within which the virus is most likely to spread that should get it, which is presumably the otherwise healthy population.

I don’t know the answer, but it will be interesting to see how this all develops. In any case as far as I can see it there’s very little prospect of high levels of population immunity being reached by this time next year. And that’s even if the vaccine is available soon, which is by no means clear will be the case. As a matter of fact I wouldn’t bet against me still having to do daily updates on Covid-19 statistics for most of next year.

 

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Dare we hope?

Posted in Covid-19, Poetry, Politics with tags , , , , , on November 9, 2020 by telescoper

A short passage from Seamus Heaney’s verse play The Cure at Troy: A Version of Sophocles’ Philoctetes has been much quoted recently. It even ended the RTÉ News last night:

The passage begins

History says, Don’t hope
On this side of the grave.

Well, there’s an additional reason for hope this morning, in the announcement of good progress in the search for a vaccine against Covid-19. The two pharmaceutical companies involved are Pfizer (USA) and BioNTech SE (Germany). The reported efficacy of the vaccine tested so far is over 90%, which is far higher than experts have predicted. Now these are preliminary results, not yet properly reviewed, based on a sample of only 94 subjects, and I’m not sure what motivated the press release so early in the process. I’m given to understand that the type of vaccine concerned here would also be challenging to manufacture and distribute, but we’re due for some good news on the Coronavirus front so let’s be (cautiously) optimistic.

On top of that it seems that Ireland at least is turning the tide against the second wave, with new cases falling every day for over a week:

Dare we hope?

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R.I.P. Derek Mahon (1941-2020)

Posted in Covid-19, Poetry with tags , , , , on October 2, 2020 by telescoper

The poet Derek Mahon has died, so it seems apt to pay tribute by posting some examples of his poetry.

This poem, Everything is going to be all right, was read on the main news on RTÉ television when the national lockdown was announced back in March, sounding a note of optimism to a worried nation. I’m not sure everything is going to be all right, but it’s an excellent poem:

How should I not be glad to contemplate
the clouds clearing beyond the dormer window
and a high tide reflected on the ceiling?
There will be dying, there will be dying,
but there is no need to go into that.
The poems flow from the hand unbidden
and the hidden source is the watchful heart.
The sun rises in spite of everything
and the far cities are beautiful and bright.
I lie here in a riot of sunlight
watching the day break and the clouds flying.
Everything is going to be all right.

Sadly he didn’t live to see the end of the pandemic. Over the years I have posted a few poems by Derek Mahon. Here are two more. This one is called The Thunder Shower

A blink of lightning, then
a rumor, a grumble of white rain
growing in volume, rustling over the ground,
drenching the gravel in a wash of sound.
Drops tap like timpani or shine
like quavers on a line.

It rings on exposed tin,
a suite for water, wind and bin,
plinky Poulenc or strongly groaning Brahms’
rain-strings, a whole string section that describes
the very shapes of thought in warm
self-referential vibes

and spreading ripples. Soon
the whispering roar is a recital.
Jostling rain-crowds, clamorous and vital,
struggle in runnels through the afternoon.
The rhythm becomes a regular beat;
steam rises, body heat—

and now there’s city noise,
bits of recorded pop and rock,
the drums, the strident electronic shock,
a vast polyphony, the dense refrain
of wailing siren, truck and train
and incoherent cries.

All human life is there
in the unconfined, continuous crash
whose slow, diffused implosions gather up
car radios and alarms, the honk and beep,
and tiny voices in a crèche
piercing the muggy air.

Squalor and decadence,
the rackety global-franchise rush,
oil wars and water wars, the diatonic
crescendo of a cascading world economy
are audible in the hectic thrash
of this luxurious cadence.

The voice of Baal explodes,
raging and rumbling round the clouds,
frantic to crush the self-sufficient spaces
and re-impose his failed hegemony
in Canaan before moving on
to other simpler places.

At length the twining chords
run thin, a watery sun shines out,
the deluge slowly ceases, the guttural chant
subsides; a thrush sings, and discordant thirds
diminish like an exhausted concert
on the subdominant.

The angry downpour swarms
growling to far-flung fields and farms.
The drains are still alive with trickling water,
a few last drops drip from a broken gutter;
but the storm that created so much fuss
has lost interest in us.

And this one, about the noble self-sacrifice of Captain Lawrence Oates,  is called Antarctica

‘I am just going outside and may be some time.’
The others nod, pretending not to know.
At the heart of the ridiculous, the sublime.
He leaves them reading and begins to climb,
Goading his ghost into the howling snow;
He is just going outside and may be some time.
The tent recedes beneath its crust of rime
And frostbite is replaced by vertigo:
At the heart of the ridiculous, the sublime.
Need we consider it some sort of crime,
This numb self-sacrifice of the weakest? No,
He is just going outside and may be some time
In fact, for ever. Solitary enzyme,
Though the night yield no glimmer there will glow,
At the heart of the ridiculous, the sublime.

Rest in Peace Derek Mahon (1941-2020)

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The Virtue of Signalling

Posted in Covid-19, Education, Maynooth, Politics with tags , , on September 3, 2020 by telescoper
I was in a supermarket in Maynooth yesterday morning when a bloke was refused entry for not wearing a mask. That’s the first time I’ve seen that happen, though I’ve heard various people mentioning similar stories elsewhere. There is a big sign near the entrance to the store saying that face masks are mandatory, which they have been for some time in Ireland, so he could not make the excuse that he didn’t know. I rather think he was trying to make a point.
The person concerned didn’t get violent, but was extremely loud and abusive to the staff, who shouldn’t have to put up with that sort of behaviour. He stood there for a while shouting expletive in between which his message was that he didn’t care whether he got Covid-19 as it was “just the flu”. I did wonder whether someone might call that Gardaí but after a few minutes, afer which he either felt he had done what he wanted to do or that he was wasting his time, he left.
I have to admit I completely fail to see why certain people find wearing a face mask such an ordeal. It’s really nothing. I understand that some people, with e.g. asthma, might have good reasons for finding it difficult but I’m talking here about people without such reasons who seem to think they’re being asked to bear some intolerable burden, rather than just wearing a piece of light material over their nose and mouth. I’ve got quite used to it and think nothing of it. As winter comes on I even think wearing a mask might help keep my face warm and, more importantly, protect my beard from inclement weather.
The only thing that bothers me slightly is that I have very boring face masks when others seem to have invested in colourful stylish affairs. It makes me feel a bit drab. Perhaps I should invest in some more glamorous masks.
But back to our friend in the supermarket. He of course may not care whether or not he gets Covid-19, but that’s not the main point of wearing a mask. Face masks are far more effective at protecting other people from your germs than protect you from other people’s germs. I suspect, however, that trying to explain this to the person concerned would simply make matters worse. To be happy wearing a face mask you have to be the sort of person who cares about what happens to other people and there are some – regrettably many these days – who just don’t. I’m sure that extreme selfishness translates into their political attitudes too.
When we return to on-campus teaching at the end of this month, students will be asked to wear face coverings in lectures. I’m not sure how that will work out. In particular I don’t know who is supposed to police it. Supermarkets have people on the door to turn away the unmasked. Are we to have that at the entrance to lecture theatres?
Lecturing with a face mask on will be difficult, but in a big theatre the lecturer is sufficiently far from the front of the audience that won’t be necessary.
I’m not sure how effective face masks will be at slowing the spread of Covid-19 – we’ll have to wait and see – but my attitude is that they are just a part of a bundle of measures, including frequent washing of hands, wiping surfaces regularly, maintaining social distancing, etc that all contribute. The great value of a face mask in all this is that it is visible. Wearing a mask is a signal to others that they should remember the danger of the situation and act accordingly. It’s a way of showing leadership.
It has become fashionable (at least among those who possess no virtues) to use the phrase virtue signalling as pejorative term for doing or saying something good in a way that is conspicuous. To the person ejected from the supermarket, the wearing of a face mask is probably an example of virtue signalling. I think it is too, literally, and I’m all in favour of it.

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Thoughts on Mortality

Posted in Covid-19 with tags , , , on September 2, 2020 by telescoper

I was updating my Covid-19 statistics page yesterday after the daily announcement and I noticed that it has now been ten consecutive days since the last Covid-19 related death in Ireland. As of yesterday there were only 40 people with Covid-19 in hospitals in the Republic, six of whom were in intensive care.

These low numbers are of course very good news indeed, but it got me wondering why. As you can see from the above graph, new cases started to increase about two months ago. In the first wave the mortality figures started to grow with a much shorter lag, although it is difficult to be too precise about it because of delays in testing and reporting that shifted the blue curve to the right.

With new cases in the Republic now appearing at an average rate of around 100 per day and assuming a mortality rate of a few percent, one might have expected to see the mortality figures rising, but this has not happened. It must be said though that the current level of new cases is much lower than the initial peak, as this linear plot (also smoothed on a 7-day window) makes clear:

An even more remarkable case is that of France (data from here):

The blue curve is a 7-day moving average. You can see that the level of new cases in France is about the same as it was in late March. The daily mortality figure however looks like this:

So the mortality rate among recent cases is much lower in France than in Ireland.

I’m not going to discuss mortality data in the United Kingdom as these are being fiddled by the Government who have arbitrarily decided not to count anyone who dies more than 4 weeks after testing positive for Covid-19 in the figures. It’s a blatant con intended to make people think that the situation in the UK is better than it actually is.

I suppose the main factor for this is that the more recent cases are not happening in hospitals or care homes and they are affecting mainly younger people who have no underlying health conditions; over 70% of the recent cases in Ireland are people under the age of 45. It may also be that the treatment of patients is more effective now that it was in March and April.

Some people are arguing on social media are saying that data such as these prove that the Coronavirus has lost its potency and is no longer a threat. In order to provide evidence in support of such a claim one would have to take account of the differences in demographic and health history of new cases versus older ones, and I have not seen such a study.

Update: I had a terrible feeling that this would happen, but the same day I wrote this a further Covid-19 related death was reported. This was however a late notification of a death that occurred in June. For the latest figures see here.

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Covid-19 in Ireland: No End in Sight

Posted in Covid-19, Maynooth with tags , , , on August 19, 2020 by telescoper

Yesterday the Irish Government put the brakes on the relaxation of the restrictions imposed because of the Covid-19 pandemic and tightened up some existing rules. The reason for this move is obvious when you look at the data:

After dropping to very low numbers of new cases a couple of months ago, the curve has been steadily rising. On Saturday 200 new cases were reported and yesterday the figure was 190. The average number of cases per day over the last 7 days is now over a hundred. The last time it was that high was in early May.

So what has gone wrong?

A large fraction of the cases appearing in the latest outbreaks is associated with either meat (or other food) processing plants and with direct provision centres. These are particularly vulnerable to outbreaks because of the difficulty of maintaining social distancing. Most of the people involved however are under the age of 40, so these outbreaks are not (yet) associated with a significant increase in mortality. Until recently it was hoped these localised `events’ could be contained by testing, contact-tracing and isolation.

Unfortunately these outbreaks are happening at a time when public adherence to Covid-19 restrictions has also been declining. I have noticed over the past few weeks that many people in Maynooth are congregating outside, especially in Courthouse Square, without any attempt at social distancing and with nobody wearing a face masks. Pubs in the area are serving drinks to take away and people are just taking them outside and treating the public areas as a big beer garden. The law it seems can do nothing about this, and pub landlords are doing nothing to discourage it.

The problem in this respect started back in June when the (then) Taoiseach Leo Varadkar decided to accelerate the stages of the Roadmap. I didn’t understand this at the time. The plan was carefully thought out and was working. Why change it? The answer is of course intensive lobbying from vested interests worried about the impact on their own finances.

Anyway, the effect of this change was immediately noticeable in that a sizeable contingent of the public clearly thought it was a signal that the Covid-19 outbreak was over and became complacent about the continuing risk of community transmission.

I think of the outbreaks in factories and direct provision centres as sparks that can hopefully be snuffed out quickly. The real risk to the public however is from these sparks spreading the conflagration into the general population. Social distancing acts like a sort of fire break – that’s what the new restrictions are trying to achieve.

What this means for the next month or so I can’t say, but I wouldn’t rule out a full lockdown being imposed again.I hope that doesn’t happen because I am looking forward to getting back to teaching, but it’s looking touch-and-go at the moment.

 

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