More microbiology news

I hinted at a bit of a viral revival just yesterday, but I wasn’t quite expecting the rest of microbiology’s greatest villians to kick in just yet. Still, they did.

Monkeypox goes Iberian:

Portuguese authorities have confirmed five cases and are investigating another 15 suspected cases. In a statement on Wednesday, Portugal’s health ministry said the cases it had detected – all in the Lisbon and Tagus Valley region – had all involved men whose symptoms included ulcerative lesions.

While in Madrid:

“Generally speaking, monkeypox is spread by respiratory transmission, but the characteristics of the eight suspected cases point towards fluid contact,” the spokesperson said.

Fernando Simón, an epidemiologist who heads Spain’s health emergencies centre, said while it was unlikely that monkeypox would spread significantly, “that can’t be ruled out”.

Salmonella in Belgian Chocolate:

Obviously not a virus, but still small and nasty, so it fits here.
This one has been going for a while now, but an updated report means that we can include it in this week’s microbiology news. Belgium chocolate is known for its quality and its creamy, luxurious taste, and now also for containing Salmonella typhimurium ST34. Delicious.

Cases, which have now started to decrease, stood at 324 (including both probable and confirmed) in the EU/EEA and the UK, as of 18 May 2022. They have been reported in twelve EU/EEA countries (Austria, Belgium, Denmark, France, Germany, Ireland, Italy, Luxembourg, the Netherlands, Norway, Spain and Sweden), the UK, Switzerland, Canada, and USA.

Polio in Mozambique:

Awful news about the first wild poliovirus infection in Moz in over 30 years.

The case was diagnosed in a child in the northeastern province of Tete, it said. “The detection of another case of wild poliovirus in Africa is greatly concerning, even if it’s unsurprising given the recent outbreak in Malawi,” WHO Africa chief Matshidiso Moeti said.
Poliomyelitis – the medical term for polio – is an acutely infectious and contagious viral disease which attacks the spinal cord and causes irreversible paralysis in children.

The virus was tracked back to the outbreak in Malawi from a strain originally circulating in Pakistan. Local countries are now desperately trying get all their children vaccinated before there is any further spread.

Corona continues:

No handy news report to go with this one, but despite the numbers starting to drop in SA, there have been three five more confirmed cases in people I know in the last 24 hours.


I’d love to see the provincial data: it’s my feeling that a significant decline from the previously high numbers in Gauteng might be masking a steady (or even slightly increasing) case load in the Western Cape. Certainly anecdotally, we’re feeling a bit surrounded by it again. A reminder to please act sensibly and responsibly because this clearly isn’t done yet.

And obviously, a get well soon to those in question. You know who you are.

And that’s it for today this particular hour as far as microbiology news goes. Join us again tomorrow for more happy happy joy joy fun and games as thousands of people get sick thanks to various germs, disease and infection.

Promise made, promise kept

“The best way to keep your word is not to give it,
I don’t make promises ’cause promises die.”

said PM Dawn in the 90s.


But I did give my word about 6 months ago:

…and so the only way to keep it was to follow through. And that’s what I did yesterday afternoon, before inviting Pastor Agony and his World of Pain Ministries to give me a day-long sermon today.

A few thoughts:

A year ago, this would have been mundane, routine. Yesterday, it took everything that I had. But I made it. And I fully recognise that it’s not a big deal to do this (and a whole lot more) for a lot of people, but these things are all relative. I’m going to slow down again now for a while. This just needed doing, it has been done, and now I can just gradually get back into gentle, shorter runs to continue to improve my fitness.

Post-Covid tachycardia is a real thing. I don’t need to go into details here, but that particular graph wasn’t particularly pretty for this run. And it continued to be particularly unpretty for quite a while afterwards.

On that note, if my heart does give up (and I really don’t think that it’s going to happen), please make sure that everyone understands that the virus is responsible:

Those with a history of COVID19 infection were more likely to have the following 12 months later: strokes, dysrhythmias (five different kinds), inflammatory heart disease (like myocarditis), heart disease (four different types, including heart attacks), other cardiac disorders (like heart failure), and clotting issues (like pulmonary embolisms).
The risks for each of these varied. For example, the risk of a heart attack was 63% higher among those with a prior COVID19 infection compared to those without an infection. The risk for myocarditis (inflammation of the heart) was 538% higher.

Don’t let the tin-foilers tell anyone it was the vaccine. In fact, go one step further and punch anyone that suggests it had anything to do with the vaccine – on my behalf, of course. Violence was never (ok, rarely) the answer when I was alive, but I see no reason to hold back now I’ve shuffled off this mortal coil.

And finally, the battle to get back to pre-Covid fitness continues. Just perhaps not at this level for the next few months.

But… I did it.

Day 665 – Who knew?

According to this article – written by a Professor of Health Sciences, a Distinguished Professor of Chemistry, a Professor of Mechanical Engineering and… er… a Research Scientist punching way above his weight – being with a lot of people, in a poorly ventilated space, without face coverings or while singing, shouting and exercising, (or any combination of the above) can result in a higher likelihood of you catching Covid-19.

This isn’t new news, of course. We’ve known all of these things for quite a while, but the authors here have come up with a way of putting a figure on each of the scenarios. They’ve even made a calculator for you to estimate your own risk in doing whatever you are doing, including how long you are doing it for.

Clever stuff.

But these are just estimates. We can’t put an exact figure on any of this. And we can’t say that being with someone silently, outdoors, with a mask on, in the breeze means that you won’t get Covid. This is a Swiss Cheese Defence, where no one single precaution will prevent transmission completely, but where a combination of efforts can limit your chances of being infected. The more precautions you take, the more likely you are to avoid getting it.

Of course, underpinning all of this is our best weapon: the vaccine. That’s the single thing you can do to protect yourself and your family more than anything else.

This is especially important to understand with the Omicron variant, given that it is so much more infectious than the previous iterations of the virus. And I know that you knew all this already, but there are an increasing number of people who are proclaiming that the pandemic is over, and thus giving up on the measures to stop it, and that is still a bit of a stretch. We’re not there yet.

Keep safe.
Avoid klapping gym boet in an overcrowded Crossfit place built in a light industrial unit.
Or going to church.

Day 620 – Myths

Just wandering back through the anals of twitter (misspelling entirely deliberate), and came across this gem from 23 May this year:

I checked back to the 23 May on a handy graph supplied by google and found this:

Look what happened just afterwards. Tweet did not age well.

Officially, there were about 30,000 Covid deaths in South Africa in the “mythical” third wave, although the excess deaths figure, which many professionals believe to be far more accurate for this sort of thing, suggests nearer 3 times that number.

Surprisingly, the same account (which ticks all the usual boxes: pro-gun, pro-Trump, anti-vax, “the media have been bought off”, “there’s graphene in the jab”, “the earth is flat”, “Fauci is the devil”, “Nuremberg trial 2022”, “Ivermectin is the answer”) is now choosing not to believe that there is a fourth wave on the way. Talk about doubling down on a losing position.

That said, in one way – obviously – I actually wish that he was right.

But of course, sadly, he’s wrong again.
I do hope that his [checks notes] 84 followers will hold him accountable for his repeated mistakes.

Day 618 – Infectiousness v Lethality

As we look at the latest figures from Gauteng, ground zero for SA’s Omicron-driven Fourth wave (again via @rid1tweets), we see this scary graph:

The hospital and death figures always lag a week or two behind, so really, all the we can say about Omicron at the moment is that it’s spreading like wildfire. Given that the conditions at the start of each of the three previous waves was pretty much the same, and that we should now have some protection from (some) previous infections and (a bit of) vaccination, we’d wouldn’t expect to see the black line rearing up like a pissed off Cape Cobra in the Overberg, rather it should be flatter, like a mole snake on the R27 West Coast Road.

It’s so steep because the virus is spreading very quickly, which suggests that it is very infectious. And that would fit with the (anecdotal) evidence I’m seeing in my friends and friends of friends in Cape Town. Every second person has suddenly got it: some not so bad, some bad, some vaccinated, some not (and some unknown), some previously infected, some not, some careful, most… you know. Mmm.

But it wasn’t here a week ago and now it’s everywhere.

Increased infectiousness = increased transmissibility.
And so the gradient of that black line is very bad news. Not least because of this:

Yep – a low percentage can still be a very big number if it’s a low percentage of a huge number.

Delta looked like a variant that you wanted to avoid because it has/had some nasty morbidity and mortality associated with it. Omicron looks like one to avoid because it has some really nasty transmissibility associated with it – and we don’t know about the morbidity or the mortality yet.

But either way, it’s not looking good.