All going well then

I might not work in a lab at the moment, but you can never quite get rid of the microbiologist in me.

Not only did I do this test from a specimen that I took from my own good self…

I also predicted the result. Correctly, nogal.

Look, I’m anything but surprised.

Given the information that I am getting from the school after last week’s trip, this is a clear case of Tour Pox. I could use the old English term: “There’s a bit of it going around”, because there is, but that won’t help anyone who has got it.

We’re going away for a long weekend, starting this afternoon, and I’m gutted that I’m not going to able to do all the stuff that I was planning on doing, but while nothing will get rid of this any time soon, a change of scenery, some fresh air and a lot relaxation – and staying away from other people! – is surely the best way to pass the time while I’ve got it.

And it’s nowhere near as bad as that episode a couple of years ago. Thank heavens.

BA 2.86

Oh good. A new variant of Covid-19. <party emoji>

If it seems like we haven’t had one of those for a while, it’s because we haven’t. Well, not an interesting one, anyway. This one though – sadly – is of interest.

Why? Well, it has 35 mutations on its spike protein. That’s the bit that our immune system recognises. 35 mutations means that it’s likely to be disguised (at least partially) from our immune systems, meaning that we’re more likely to become infected with it: even if we’ve had the vaccine or if we’ve had Covid (of any variant) previously. It doesn’t mean that we won’t have any defence against it though. More likely just a bit of a slower, poorer one.

We don’t know a lot at the moment: we’re not really looking for Covid as much as we have been before, so this could be sneaking in a bit under our radar. We’ve only seen 9 cases* in 5 countries, which seems like nothing, but at least 6 of those cases have no travel history, suggesting that they acquired the virus locally to them. It can’t just have appeared from nowhere: that indicates community spread.

And those 9 cases (UK, Demark, USA, Israel, and now South Africa) show very similar genetic sequences. That means that they haven’t had much time to mutate or change, and that indicates a rapid spread.

We’re not seeing millions of hospital admissions though, which might (hopefully) mean that this is not going to cause serious illness or mortality. But it’s likely there just isn’t enough of it yet for that to be a foregone conclusion. It is being found in wastewater screening, which probably means that there is a growing reservoir of undetected cases out there.

Honestly, scientists have been waiting for the next wave. There was never any chance of Covid just going away. And we’re still (yes wow, “still”, even after 3½ years, lol), in the early equilibrating days of what will almost certainly be a long-term virus/human relationship. Each party is still weighing up its opponent and figuring out its next move. Metaphorically, at least.

It remains to be seen if this variant will trigger a new public health crisis or will fall away without troubling us too much. At this point, the jury simply doesn’t have enough information to make any decision, and so we wait and we keep learning from the information we can get.

At the moment, it’s very much watch this space. And maybe hope for a not guilty verdict.

* I had to update this figure twice while writing this post.

Poo studies return – and they’ve got some worrying news

Truth be told, Poo Studies never went away. It’s just that – thankfully – they haven’t had very much to tell us about recently.

It does look as though that has changed recently, though.

Poo Studies is the fun name for the SAMRC surveillance programme for SARS-CoV-2 RNA in more than 80 wastewater treatment plants across 6 provinces in South Africa. Basically, as the link above describes, we can accurately predict the future when it comes to local Covid-19 infections simply by looking for bits of the virus in the wastewater (sewage) in the vicinity. It gives us a 1 or 2 week heads up notice on any impending wave of Covid-19 infections, and therefore up to three weeks on increased hospital admissions.

But while our wastewater has been tested very regularly for quite a while now, there’s really been nothing to tell us about. Until now.

And if you think that Cape Town is a steep rise, wait until you see what they’ve been excreting in Worcester, just on the other side of the tunnel:

To me, that actually looks like someone dropped some virus into the thermocycler. I’m intrigued to see if that is actually a genuine result, although that little rise between 19/09 and 26/09 does do a bit of groundwork. If it is genuine, well, no-one is saying that we’re all going to die or anything, but it shouldn’t come as any surprise that Covid levels are rising again. This is, as we’ve seen throughout the pandemic, the MO of this viral infection. But that sort of increase is a bit concerning.

But what variant will this be? And how will it affect South Africa with its under-vaccinated, over-exposed population. My microbiology senses are tingling with mounting anticipation (and a teeny-tiny amount of dread).

Blame the virus

There’s a worrying thing happening worldwide at the moment. Anecdotally, we’re seeing a lot more people suffering from – and/or dying from – cardiac problems. Generally, these people tend to be relatively young, and often relatively fit. Certainly not the cohort you would expect to be hit in this way.

Of course, the tinfoilers are all over this. After all, what has changed since the onset of the Covid pandemic? Yes, the vaccine. So that must be it, because there’s nothing else that has been so ubiquitously distributed around the world (ha!), so QED, the vaccine is causing the problem.

You actually have to admire their scientific approach. Indeed, when we as scientists are trying to find out what causes something, we too look at changes in the systems which precede that thing. In this case, what we would also consider is:


And lookie here: this German study suggests that infection with Covid – even if it’s a mild infection – is associated with heart problems down the line.

And, surprise surprise, they found damage to the heart and increased cardiac markers (the chemicals in the blood that we measure to see if there is damage to the heart) in previously healthy patients.

This is a study that still needs more work (indeed, it’s still ongoing), but the signs are clear. If you have had Covid, you are more likely to have cardiac damage than if you didn’t have Covid. And while in many cases, that might only manifest itself in shortness of breath or chest pain, there will sadly be some individuals who suffer much more serious consequences. See my first paragraph above.

These observations fit well with another study – importantly mostly done before the vaccine was widely released – in which a team based in St Louis, USA found some very disturbing results regarding cardiac and circulatory problems post Covid infection:

Importantly, the more severe the infection (they used non-hospitalised, hospitalised and ICU) the greater the increase in risk, but in virtually every situation, the risk of heart or circulatory disorders was increased in those who had been infected with SARS-CoV-2.

So when we’re out there considering whether to take our booster jab for Covid, please look beyond the anti-vax nonsense. Please ignore the shouty people telling you that “the jab is killing healthy, young people”. No. It’s the damn virus that’s doing that.

And if you want to be better protected against the damn virus, go get the jab.

Fewer updates

Fewer because the NICD is stopping its daily Covid reporting, and moving to a weekly report instead:

And with that, Ridhwan Suliman’s daily reporting of the NICD’s daily reporting also comes to an end. Well done on a sterling effort throughout the last two (plus) years.

Why these things? Well, because Covid isn’t a big thing in SA at the moment. It has been a big thing in 5 very separate waves:

But it’s not anymore/at the moment.

There are some thick people out there asking where the next wave is now that the mask mandate has been removed in SA, but the fact is that the mandate was removed because there was virtually no Covid around. And while I don’t think there’s any question that we are in a low Covid moment right now, it’s worth noting that there’s likely still a great deal of under-reporting, given that the public don’t have access to Covid tests, and have to pay a few hundred Rands to get one.

No-one has any money and there’s very limited value in doing a test when you aren’t going to act on the results. If you are sick, you’re going to stay in bed anyway. If you aren’t sick, why are you getting tested (aside from the tiny, tiny number who require it for travel)? To spend hundreds on a test, when the result doesn’t matter… well, it’s no wonder that the case numbers are so low.

What next? Who knows… If this virus is going to become seasonal like we’re all being told, then I’d like to know when, exactly. At the moment, it’s still circulating, mutating, and working according to viral timeframes, rather than seasonal ones. And “we” are seemingly happy for that to happen, while it knocks off a 9/11 number each and every week in the USA with virtually no news coverage. Have “we” decided that that’s an ok situation? Are “we” content with that?

I’m not, because there is clearly more to this virus than just that week/fortnight long acute nastiness. We’re learning about more and more complications and long-term effects of Covid every day, and we don’t have anything in place to handle them or mitigate for them.

That’s not good.
And very possibly not sustainable, either.