Archive for SARS-Cov2

Second Booster

Posted in Biographical, Covid-19 with tags , , , , on September 22, 2022 by telescoper

Today I took a trip out to Punchestown Racecourse for my second Covid-19 booster jab. The possibility of booking one of these opened up for my age group (55+) a few weeks ago and I booked one straightaway, but I was advised to postpone it because of a mystery ailment. That now having cleared up I decided to have it done today, ahead of the full start of teaching next week. In the meantime the booster process has been opened up to mere youngsters (50+) but it was easy to get an appointment.

As far as I know I have ever caught Covid-19, but I thought it wise not to take any chances with the new influx of students and the possibility of increased infection levels. My first booster was on 15th December 2021, so protection is likely to have waned considerably since then. As you can see, new cases have been falling recently in Ireland but the level of new infections (7-day average around 230 per day) is still quite high:

My previous jabs were at City West so I was a little surprised when I registered for my second booster that I was directed to Punchestown. It’s about the same distance from Maynooth to either venue, though, and when I got to the racecourse it was very quiet and I was in and out within half an hour (half of which was the 15 minute “recovery” period). The racecourse – used for steeplechases – is heaving at the time of the annual Punchestown Festival, but fortunately I didn’t have to dodge either crowds or horses, though it was raining heavily.

This time I had the Pfizer-BioNTech vaccine (“Comirnaty”), same as my two original shots; my first booster was of the Moderna (“SpikeVax”) variety.

I’ll be working from home this afternoon in case of problems (though I didn’t experience any serious issues with previous jabs). My next lecture is at 11am tomorrow (Friday) so I should be fine by then even if I experience any side-effects this afternoon.

Meanwhile, back at Covid…

Posted in Covid-19, Maynooth, Politics with tags , on July 6, 2022 by telescoper

While the Tory Government on the other side of the Irish Sea appears to be collapsing I’ve trying not to laugh too loud so have distracted myself by updating my Covid-19 page with the latest data for Ireland. The summary figure is this:

You can see that cases (blue curve) are still rising (up 5.8% on last week) but the increase may just be slowing. I only show PCR-confirmed tests so interpretation of these is complicated by the lack of general PCR testing. The testing positivity rate is 38.5% and there are many more positive antigen tests not confirmed by PCR. There are now over 900 people in hospital with Covid-19 and 37 in intensive care. The mortality rate (orange curve) however remains steady.

I’m a bit concerned that case numbers are so high, especially as there are so few people taking precautions. I know this is purely anecdotal but I do know several people in Maynooth who have come down with fairly nasty doses of Covid-19 in recent weeks. I also know of many people who have travelled to conferences for the first time in a couple of years only to come down with Covid-19 in the process. The high incidence of Covid-19 is causing staff absences elsewhere that are disrupting many organizations and businesses. I do hope we’re not in for another surge before the start of term in September!

Despite all this (and the fact that I have been fairly lax about wearing a face covering myself) I still have not experienced Covid-19. I’ve never had symptoms and never tested positive. Have I just been lucky, or is there more to it than that?

Concerning Covid Immunity

Posted in Biographical, Covid-19, Maynooth with tags , , , on June 10, 2022 by telescoper

Over the past few weeks I’ve attended a number of events at which most people were not wearing face coverings, including a recent Open Day at which I took my mask off in order to be heard in a very crowded space. Although I still wear a mask on public transport and in shops, most people now do not.

The first thing I’d note is that that there has been a clear upturn in reported Covid-19 cases, with figures now running at about 700 per day:

(Official figures for Ireland are only issued weekly these days…)

It’s not an alarming increase but hospitalizations and testing positivity are also increasing, though the mortality rate remains low because of the protection afforded by vaccines. Incidentally, it was a year ago on Wednesday (8th June) that I received my second Pfizer dose. One wonders how long vaccine protection will last, though, until further boosters are needed. If cases continue to rise I wonder if any measures will be put in place before the start of next academic year?

A number of my colleagues at home and abroad have attended scientific conferences recently, a number of which have led to mini-outbreaks and some instances of quite serious illness. Although most people seem to think Covid has gone away, it clearly hasn’t. A resurgence is all we need right now.

Anyway, one of my colleagues at work expressed surprise that I didn’t catch Covid during the largely unmasked Open Day at the end of April. Of course I might have done but I certainly didn’t display any symptoms. I’ve actually been quite surprised that I have never shown any sign of SARS-Cov2 at all during the entire period of the pandemic, while many of my colleagues and students in the Department have come down with it.

Coincidentally, a comment appeared yesterday on a blog post I wrote a while ago in which I revealed that I have the  CCR5-Δ32 genetic mutation which confers protection against HIV infection. As a matter of fact I have it twice (i.e. homozygotic). For one thing the commenter pointed out that this mutation may have protected against smallpox, which means some evolutionary selection may have been involved in its propagation. The commenter also drew attention to the evidence – by no means conclusive at this stage – that this mutation may also protect against Covid-19. If you’re interested here are links to some papers:

The last of these is a preprint but the other two are peer-reviewed publications.

Could it be that I’ve yet again been a jammy bastard and inherited immunity to Covid-19 too?

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…