Archive for SARS-Cov2

End of Term Blog

Posted in Biographical, Covid-19, Education, Maynooth with tags , , , , , on December 18, 2021 by telescoper

Yesterday was the last day of teaching at Maynooth University for 2021 and, although I didn’t have any teaching to do, I walked to the Department partly to get a bit of fresh air having been stuck at home on Thursday after my booster jab, and partly to collect a few things before the break. I also discovered that a lovely parcel of goodies had been sent to me and I was anxious to collect the items before Christmas.

I’ll be keeping myself to myself over the break, apart from the odd trip to the shops, and am glad to be doing so. We are yet to see the steep increase in Covid-19 cases associated with the omicron variant happening in the UK and elsewhere in Europe. If anything case numbers are currently declining slowly. But the new wave will undoubtedly hit Ireland soon.

UPDATE: not half an hour after I posted this, the HSE announced 7333 new cases of Covid-19 in Ireland, more than double yesterday’s figure and the highest number seen since early January. And this is before the Christmas surge.

The jury is still out on whether omicron is more or less dangerous than previous variants but it is clearly more transmissible, and I don’t see the point of taking chances, so I agree with the Irish Government on the need to take precautions. I don’t think the latest restrictions go anywhere near far enough though.

Yesterday we received at work an email from University management that said, among other things, that

At present the aim is to resume teaching on 31 January, as in Semester 1.

The phrase “as in Semester 1” means that large lectures will be online-only but everything else will be face-to-face. That is a reasonable starting point because the extent of the omicron wave is as yet unknown, but I think it’s more likely than not that in the end we’ll find ourselves doing everything online. I just hope a decision on that is made in reasonable time for us to put Plan B into action. We don’t start lectures again until January 31st and there should be enough data by then to make an informed decision.

I don’t want to sound unduly pessimistic but I don’t see any sign that we are anywhere near the end of this pandemic. With a bit of luck we might find that we’re roughly halfway through, but as long as governments allow large pools of virus to circulate, mutations will continue to occur and new variants will continue to emerge. To end this cycle will require a majority of the world’s population to be vaccinated, and I don’t see that happening soon.

The Coronavirus Vaccine Effect

Posted in Covid-19, mathematics with tags , , , , , , on December 12, 2021 by telescoper

When I was updating my Covid-19 page today I thought I would try something a bit different. Here are the cases and deaths (in the form of 7-day rolling averages) as I usually plot them:

You can see a slight recent downturn – the latest 7-day average of new cases is 4214.3; it has been falling for a few days. A log plot like this shows up the changing ratio between deaths and cases quite well, as in l if you multiply a quantity by a factor that manifests itself as a constant shift upwards or downwards. There is clearly a bigger shift between the orange and blue curves after 500 days than there is, say, between, 300 and 400.

(I don’t think you can read much into the gap between the curves at the beginning (up to around 100 days in) as testing coverage was very poor then so cases were significantly underestimated.

Anyway, to look at this a bit more clearly I plotted the ratio of daily reported deaths to daily confirmed cases over the course of the pandemic. This is the result:

The sharp downward glitches occur whenever the number of reported deaths is zero, as log of zero is minus infinity. The broader downward feature after about 300 days represents the period in January 2021 when cases were climbing but deaths had not caught up. To deal with that I tried plotting the deaths recorded at a particular time divided by the cases two weeks earlier. This is that result:

The spike is still there, but is much decreased in size, suggesting that a two week lag between cases and deaths is a more useful ratio to look at. Note the ratio of deaths to cases is significantly lower from 500 days onwards than it was between 200 and 400 (say), by a factor a bit less than ten.

This obviously doesn’t translate into a direct measure of the efficacy of vaccines (not least because many of the recent cases and deaths are among the minority of unvaccinated people in Ireland) but it does demonstrate that there is a vaccine effect. Without them we would be having death rates up to ten times the current level for the same number of daily cases or, more likely, we would be in a strict lockdown.

On the other hand if cases do surge over the Christmas period there will still be a huge problem – 10 % of a large number is not zero.

A Date for a Boost!

Posted in Biographical, Covid-19, Education with tags , , , , on December 9, 2021 by telescoper

After expressing concern about the prospects of getting a timely booster jab last night I received an SMS message offering me an appointment next Wednesday for a shot. The text was sent on 8th December, six months to the day since my second jab (8th June). I will once again have to travel to City West in order to receive it, so will have take some time off work but that’s a small price to pay.

I had inferred (incorrectly) that it would take much longer to get a date for booster because most of the people I know in their sixties haven’t had theirs yet and they are higher priority than me. I now realise that may be because they had the AstraZeneca vaccine, which had a longer interval between first and second doses than the 4 weeks for the Pfizer vaccine I had, so had a later second dose than mine.

My third vaccine dose will be of the Moderna vaccine; the previous two were Pfizer/BioNTech. It seems everyone who is getting a shot this month will be getting the Moderna version as Ireland has a large stock of this vaccine due to expire next month. Although its efficacy against the omicron variant is unknown, I will of course attend the appointment.

Yesterday, before I received the text message announcing my booster shot, I emailed the students in my classes to say the remaining lectures of the term will be online-only because of the high levels of Covid-19 in circulation and my waning immunity. Next week’s booster doesn’t change that as next week is the last week of teaching. My plan is to do the lectures live as webcasts and make the recordings available afterwards, which is how I’ve done them the entire term, except I’ll be doing them from home with no in-person audience. Apart, that is, from next Wednesday, when I’ll only be able to offer a pre-recorded lecture as I’ll be at City West when the lecture is scheduled. That will be my last lecture of the Semester, as most of my teaching is concentrated in the early part of the week.

Owing to a combination of Covid-19, Storm Barra and no doubt sheer exhaustion, student attendance at lectures and tutorials on campus has fallen sharply, though attendance at my second-year class has remained quite high. On Tuesday the campus was virtually deserted but about 70% of my class for Vector Calculus & Fourier Series were there. Somehiw, though, I don’t think they’ll mind too much watching the remaining couple of lectures from the comfort of their homes!

Half Measures

Posted in Biographical, Covid-19, Education, Maynooth with tags , , on November 16, 2021 by telescoper

Against the backdrop of rapidly rising numbers of Covid-19 cases the Irish Government today announced the return of some restrictions, including the closure of hospitality venues no later than midnight and a return to working from home “unless absolutely necessary”. On the latter, however, it has said that “There will be no reintroduction of remote learning for schools and third-level institutions at this point”.

I think the key phrase is “at this point”. I don’t think the new measures go nearly far enough and they will have to be revisited in a week or two, at which point we will revert to remote (online) teaching. Although we haven’t been give guidance yet, I think we’ll be carrying on with in-person lectures and tutorials at Maynooth for the time being, but it’s no more than an even money bet that we’ll stay that way until the end of term. I would also suggest that the odds are very much against us actually having examinations on campus in January. We await further guidance from the University about this, so I don’t know. The timetable for the January examinations is due to be published next week so a decision will have to be made very quickly.

What I do know, though, is that my second vaccine dose was on June 8th. The Government has now announced that 50-59 year olds (which includes me) can now get a third (booster) dose six months from their last one. In my case that is December 8th. But the roll-out of boosters has been painfully slow in Ireland, and most of the over-60s haven’t had theirs yet. It’s likely to be weeks or months until I get an appointment for mine.

We might have to switch to remote teaching in a while anyway if the rules are changed but I have made the decision that if I haven’t got my booster by December 8th I’ll be working from home and switching all my lectures online. Term ends on December 17th so I’ll only have to give a few remote lectures, but for me it is a matter of principle.

By deciding that in person teaching is “absolutely essential” the Government has admitted that lecturers are frontline staff and we should accordingly get a booster dose at the appropriate time. I’ve worked countless hours of unpaid overtime during this pandemic and I’m not going to continue without adequate protection from infection.

Worrying Times…

Posted in Biographical, Covid-19, Education, Maynooth with tags , , , on November 14, 2021 by telescoper

So here I am, trying to plan my teaching for next week and wondering what’s going to happen between now and the end of term. Here at Maynooth University lectures finish on 17th December, five weeks from now. I’m just about on schedule to cover everything I’m supposed to, so I’m not worried about that.

What I am worried about is that Covid-19 cases are continuing to climb. The latest 7-day rolling average of new cases is over 3900 per day and the increasing trend show no sign of slowing down. It will reach the 5000 mark in a week or two. Some daily figures have already passed that milestone. The death rate is still relatively low – 74 Covid-19 related deaths were recorded in the last week – but is edging up; over a hundred people with Covid-19 are being treated in ICU as of today.

The Irish Government seems to have no intention of introducing effective countermeasures and is instead just advising people to cut down the amount of socializing they do. I don’t think that will work. It seems very clear to me that the Government lost the room many weeks ago by frequently implying that the Covid-19 pandemic was over. They then caved in to the hospitality industry by allowing nightclubs to open. It is no doubt in such places that the virus is spreading. The Government keep stating that they are concerned but do nothing, blinking at the onrushing disaster like rabbits caught in the headlights of an approaching car.

Case numbers on campus at Maynooth remain fairly low, though the latest figure (69) is almost double last week’s figure (35). Students in my classes continue to wear face coverings and observe the other protocols and all the signs are that lecture halls and labs are pretty safe environments but we have no say in what happens off campus. As well as being concerned for the health of students and staff, I have particular worries about my Department. We’ve been short-staffed since the start of term and simply have no spare effort to provide cover for lectures or tutorials if anyone becomes sick.

The Irish Health Service is under extreme pressure and the delivery of booster shots is being rolled out very slowly. I had my second Pfizer dose in June so should get a third shot in December but it is not clear that I will. I’m not going anywhere at Christmas anyway so that’s not a big deal but I’m worried by the broader picture. A cartoon in a recent issue of Private Eye is very apt:

Might we have to switch our lectures back online again before Christmas? Might our examinations be online again in January? Who knows. We’ll just have to wait and see but I think the blackboard in my study might be back in use very soon.

A Year at Home

Posted in Biographical, Covid-19, Maynooth with tags , , on August 26, 2021 by telescoper

I was reminded this morning that it was a year ago yesterday that I received the keys to my house in Maynooth. I didn’t move in straight away as the house was empty and I had paid the rent on the flat I was living in until the end of August, so I moved my things gradually over the course of a week or so. Looking through all the paperwork this morning I found the pictures that the Estate Agent had used to advertise the property. Here are a few of them:

You’ll see that the bookshelves in the sitting room were empty at the time. They mostly still are. I didn’t think this time last year that I’d still be waiting a year later for my belongings to arrive from Cardiff, but at least they are in transit now. Delivery is pencilled in for next week, as a matter of fact; doing the removal on the cheap as a return load meant waiting a few weeks. I am looking forward to filling the shelves with my books (20-odd boxes of them) and putting up my own artwork. I’ve had enough of bare walls.

This morning our weekly Faculty Executive meetings resumed, the main topic of discussion – as it was this time last year – being the plans to return to on-campus teaching next month. I thought it would be interesting to show a comparison between the Covid-19 figures in Ireland on August 25th 2020 and August 25th 2021:

You will see that the daily case numbers in Ireland are currently about a factor 20 higher than they were this time last year: yesterday we had 2051 new Covid-19 cases in Ireland; a year ago there were 92. That is significant because the effect of vaccines in suppressing serious illness is at most 95%. Since the number of cases is up by a factor of 20, in some sense the risk level if everyone in the population were vaccinated would be about the same now as it was this time last year. And of course not everyone actually is vaccinated, and not everyone will be by the time teaching starts again on 20th September.

Last year the case numbers increased substantially between August and September meaning that we went back into lockdown in October. We don’t know whether or not case numbers will increase again this year, of course, but from the point of view of resuming teaching we’re really in no better shape now than we were at this time last year. Our optimism then was misplaced and that may well be true now too. This is why so many people in the University system are nervous about the edicts we have been given to return to full lecture theatres with no social distancing, no mandatory masks, and no vaccination certificates. This seems like asking for trouble.

On a personal note, I am pleased to report that the mild symptoms I mentioned on Monday have completely disappeared and, to no surprise at all, my PCR test came back negative. It may or may not be relevant that the weather has improved greatly over the last two or three days. I have now come to the conclusion that what I had was some form of seasonal allergy, possibly connected with crop harvesting in the area spreading pollen or fungal spores. The latter are more prevalent in damp or humid weather, which might be the reason for reduction in effect now. Or it could just be that a nearby farmer has stopped doing whatever he was doing. I don’t know enough about field theory to be certain.

Anyway, all of this means I can now stop self-isolating and start returning to campus again. To be honest, though, it was rather nice self-isolating at home as I spent most of the time working in the garden…

Vaccination for Lectures?

Posted in Covid-19, Education, Maynooth with tags , , , , , on August 20, 2021 by telescoper

The full guidelines on the return to on-campus teaching in September that I referred to on Monday have now been distributed to all staff, not without comment.

Basically the new advice is that in-person teaching will return in September (in fact a month from today in Maynooth) for all forms of class except lectures containing over 250 people, which will be online. Lecture halls and labs will be at full capacity, i.e. with no social distancing requirement. Students will be “asked” to wear face coverings, but we are told not to attempt to enforce this. Importantly, there will be no requirement for students to have been vaccinated in order to attend lectures.

In Ireland there is a vaccination passport system so that those who wish to dine indoors at a bar or restaurant have to show vaccination status. Perhaps someone can explain to me how it makes sense for this to be a requirement in a restaurant while it is not a requirement for a student having to sit for an hour in close proximity to up to 249 others with no social distancing and no mandatory face coverings.

This conundrum is taken to another level of absurdity when you consider that a student wishing to get lunch indoors on campus will presumably have to show their vaccine passport?

There is an article here that argues that a safe return in the presence of the delta-variant requires 90% of the student population to have been vaccinated.

A more acceptable plan would have students show their vaccination status when enrolling on the course. Those who are unvaccinated but willing to have a vaccination shot could be vaccinated there and then and be allowed to attend lectures when the vaccine takes effect. Or I should say “could have been” because the facilities required to do on-campus vaccinations have not been set up and now there probably isn’t time. Those that refuse to have a vaccine should attend lectures online on a permanent basis.

(How such a scheme would be policed is a difficult question: we don’t usually have people on the doors of lecture theatres checking student IDs or anything and there is a far greater rate of traffic at the start of a lecture than you would have at a restaurant…)

There will of course be some students who are at very high risk and should not be attending lectures anyway even if vaccinated. For them we should be providing lecture recordings. Unfortunately I don’t think we have good enough facilities to record live lectures from theatres as there has been inadequate investment in cameras etc. If we’re told we have to provide lecture recordings, for many of us that means doing the lectures twice. And so our workload increases.

On the other hand it seems increasingly likely to me that all this will be irrelevant. New case numbers are running at about 1800 per day, a level that the HSE admits to being “unsustainable”. When the first colleges return in September, a substantial surge can be expected and everything will be back online anyway.

It’s like déjà vu all over again…

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…

Reasons for Optimism

Posted in Biographical, Covid-19, Education with tags , , , , , , on July 6, 2021 by telescoper

After an interruption of almost two months because of a Cyberattack on the Health Service Executive’s computer system, daily updates of Ireland’s vaccination statistics have at last resumed, including via the Covid-19 app (which has been moribund since 11th May).

You might think it strange but I find the restoration of daily updates reassuring. I suppose it’s because I work in a quantitative discipline but I like having things expressed in figures, though I am of course aware of their uncertainties and other problems involved in interpreting them.

The latest figures above show that about 70% of the adult population has received at least one dose while about 50% have had two doses; the latter are regarded as “fully” vaccinated as are the smaller number who have received the one-shot Janssen vaccine produced by Johnson & Johnson. Although the Government missed by some margin its target of giving one dose to 82% of the adult population by the end of June, I find myself much more optimistic than in past few weeks about how things are going.

Two developments in particular have helped.

First the Government is set to purchase about a million doses of Pfizer/BioNTech from Romania. That would be enough to fully vaccinated about 10% of the population. These doses have become available because take-up in Romania is very poor and the shots would go to waste if not disposed of elsewhere. What’s bad news for Romania is, however, good news for Ireland.

The second change is that the Government has decided to allow the AstraZeneca and Janssen vaccines to be used on adults in the age range 18-34 and that vaccinations of this group are now being carried out by pharmacists. Previously these vaccines were only to be given to persons aged 50 and over. Indications are that there is some reluctance among the younger cohort, which is hardly surprising since it was only a few weeks ago that they were being told these vaccines were too risky, but I suspect this change will go a long way towards fully vaccinating the adult population, which may be possible by the end of August.

I regard the immunization of students next year’s intake to third level education institutions as a necessary condition for opening up campuses to something like “normal” teaching. Just a couple of months ago I didn’t think this would be possible, but now it might be. It’s still possible that there will be disruptions in supply but it’s looking reasonably good at the moment based on the arithmetic of how many doses are available.

The fly in the ointment is of course the so-called Delta Variant, which has already gained a foothold in Ireland and is set to cause case numbers to rise substantially. We will soon see whether this causes an increase in hospitalizations and deaths. The most vulnerable should be protected so the probability of a case turning into serious illness or death should be much lower, but we don’t know by how much. Unfortunately the statistics of Covid-19 are still not being reported publicly. Some people seem to think this means they’re not happening. It doesn’t. It just means the system for reporting them is not working. I expect the forthcoming announcement of the backlog will cause some alarm.

The Irish Government recently decided to pause the gradual reopening of the economy to allow vaccinations to proceed further. There is still a race between the Delta variant and the vaccination programme. The number of people vaccinated increases approximately linearly with time, while the number of Covid-19 cases grows exponentially in the growth phase of the pandemic. I think the pause was sensible.

Across the Irish Sea there is a different situation. The English Government has decided to abandon all attempts to control the spread of Covid-19 at precisely the point when the pandemic is in another exponential phase. The number of cases is now likely to increase dramatically. The number of resulting deaths may be fewer than in previous waves but won’t be zero. Perhaps more importantly, allowing a huge pool of virus to develop increases the chance of yet another variant evolving, perhaps one that can evade the defences afforded by vaccination even more effectively than the Delta variant. I shudder to think of the consequences if that does happen. Perhaps it already has.

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.