Day 236 – Happy Birthday to…

Happy 1st Birthday to the SARS-CoV-2 virus (you may know it by its stage name: “Corona”).

Yes, according to this March 2020 report in the South China Morning Post, the first case of Covid-19 – it’s a disease of which you might have heard mention – was identified in a 55 year old man from Hubei on this very day last year. So I suppose it’s actually Happy Birthday to the disease, rather than the virus, but by this time, who even cares about minor details like that?
You get one, you get the other.

A lot has happened since that guy decided to go for the fresh bat soup instead of the beef with noodles, hey?

55 million cases. 1.3 million deaths.
And those are the ones we know about.

And even though we’re twelve and half thousand kilometres away from the source and start of the outbreak, tucked away here in the bottom corner of Africa, we’re still on [check notes] day 236 of an ongoing state of disaster and lockdown. What an incredible timeline. What a weird world.

What a horrendous year.

To be honest, I much preferred those halcyon 120 days when the disease was raging in other places that weren’t here. But then I think we all much preferred those even more halcyon days when it wasn’t raging anywhere.

It’s not often that one can pinpoint the exact day that a new disease appears: most of the stuff that we get infected with has been around for hundreds of thousands of years. And so, despite the appalling toll which it has brought upon the entire planet, as a microbiologist, it seems almost required that this day is marked somehow.

It’s done. Let’s revisit this on November 17th next year.


EDIT: Oh wow. And look who shares this big day…

Cue the “who’s done the more damage to South Africa?” comments…


Day 151 – I’m not saying don’t do it, but …

…this microbiologist is staying away for just a little while longer.

Level 2 lockdown, arriving last Tuesday, means more of the economy can open up again. Balancing viral infection versus economy, the scale and effect of each, and retrospectively examining what should have been done has become a divisive, bitter and typically polarised debate, and is for another post, another time and – quite possibly – another person.

So that’s really not what this is about.

Gym is what this is about.

Gym is somewhere that I used to go several times a week BTV and is something that I generally enjoyed. A quick cycle here, a quick sprint there and some lifting of generally rather heavy things meant that my gains were lekker, boet* and my body was literally flooded with several (or more) endorphins, which was very nice.

My gym reopened this week, but I’m not going back.

In my considered (some might even say “professional”, but let’s not push things unnecessarily) opinion, gym is not a safe place to be right now.

There are two reasons for this.

The first one is a South African reason: the government’s hand has been forced on relaxing the lockdown. We simply do not have a strong enough economy to continue limiting business and “normal life” anymore.  SA’s infections have spread in different places at different times, prolonging lockdown: we were almost through the storm here in the Western Cape, while it was only just beginning elsewhere. And while a lot of the graphs and statistics show that we are probably past the worst, in all likelihood, if government policy was to use a harder lockdown to avoid further spread of Covid-19, they would probably have chosen to leave that harder lockdown in place for a while longer yet. (As I said, the argument about whether lockdown is/was a good thing is for another time and place.)

Thus, the virus is still very much with us and, given this opening up of bars, restaurants, businesses, and yes: gyms, it’s likely that we’ll see something of a resurgence in infections over the next few weeks. We’ve seen this pattern all over the world. In our case, this resurgence is likely to be somewhat worse than we might like, because we still have a significant number of cases circulating, meaning that the pool of potential infection is larger than we might like.

Secondly (and sadly), going to gym is one of those activities during which you are more likely to get infected with SARS-CoV-2. Nothing personal against gyms, it’s just one of those things.

This piece (shared by the NICD, nogal!) shares some of the reasons why gymming is higher risk than other things you could be doing.
It’s a list whose contents you might have seen on this blog before.

Gym is inside.
People breathe more deeply when exercising, potentially spreading more virus, and further.
You cough and splutter more as you push your exercise (see above).
Gym is full of smooth, metal, high frequency touch surfaces: weights, bars, handles etc etc. These are great surfaces for the virus to survive on.
When you sweat, you touch your face more. And when when you touch your face, you’re more likely to spread the stuff you picked up from the surfaces to somewhere where it can enter your body (eyes, nose, mouth).

It’s an infectious virus’ paradise.

And then we have the human element. Because while there are a lot of things you can do to mitigate that higher risk, you’re also relying on other people in the gym doing them too.

And to be honest, that’s not going to happen.

Masks are not going to worn (at the very least, not worn properly).
Equipment is not going to be cleaned after each use: we’re supposed to do that already and virtually no-one does.
Social distancing is not going to be respected: no-one does it in shops or anywhere else, why would they manage it here?

The cleaning team at my gym are actually noticeably brilliant. Happy, helpful, unintrusive and really, really thorough. But how are they going to keep up with people swapping machines left, right and centre? And if they can’t keep up, how clean are those machines going to be, and many of those privileged, “healthy” gym members are going to wait for 30 seconds or a minute or however long and not just shrug and get on with their workout?


For all those reasons, it is, sadly, just not a safe situation.

I like my gym and I miss my gym, and of course, if you feel the same and you want to go back: that’s entirely your call.


I’m not saying don’t do it, but this microbiologist is staying away for just a little while longer.


* they weren’t; and I don’t speak like this at all. 

Day 98 – Poo studies

Here’s some news about poo studies! Yummy.

A few other facts first.

If you go for a Covid-19 test (which you actually can’t do now, because even our fancy schmancy, first world, private laboratories are completely overwhelmed), you will have a swab thrust into your head (hopefully through one of the holes in your nose) and that swab will be sent to the laboratory.

At the lab, they’ll wash the bits of stuff off the swab, apply a few chemicals to the juice, wave a  magic scientific wand over the little test tube and and put it into a machine which looks for a specific chunk of the RNA – one which is usually tucked inside the SARS-CoV-2 virus. The chunk of RNA that the machine looks for is only found in the SARS-CoV-2 virus, so it won’t detect any of your DNA or RNA, nor the genetic bits of anything that you’ve been snorting recently.


The thing is, you can find this section of RNA anywhere that the virus is (like up your nose), just by looking for it. And equally, because it’s so specific to this virus, you know that wherever you find these chunks of RNA, that’s indicative that the virus is there.

For the purposes of this post (and basically all of the scientific rationale behind Covid-19 testing):

Chunk of RNA = SARS-CoV-2 virus

Hold that thought.

Next up: one of the big problems with this pandemic stems from the fact that (even if you have enough tests to go around), we have people who don’t know that they have got the virus (because they show no symptoms), but who are passing it on. And because those people aren’t unwell, they don’t go to get tested (because why would you?), and so we actually have very little idea how many people in any given community actually have the virus. This makes it difficult to work out how many people are likely to be sick in that community and that makes if difficult to successfully and efficiently allocate resources. Ugh.

There’s some good news though: when we are infected with viruses (yes, including SARS-CoV-2) – whether or not we are showing symptoms – we poo out viruses (yes, including SARS-CoV-2). And, as we’ve already deduced above, we can look for SARS-CoV-2 anywhere, just by looking for that bit of RNA.

Are you going where I’m going here? Yes: down to the local sewage farm.

Mariana Matus has spent years studying what comes out of human bodies in order to better understand what is happening inside us. The computational biologist helped develop heavy-duty devices that are about the size of a milk crate and can be lowered into manholes to dangle over wastewater:steadily sucking up a stream of urine and feces through a straw-like tube.

Is it lunchtime yet?

The process in the lab is just about the same as if they were testing you, except that instead of doing the science with a swab from up your nose, they do it on some poo juice.

Even better news is that it seems that an uptick in the amount of RNA (and therefore the amount of virus) in the community’s sewage predicts an increase in local Covid-19 cases by about a week.

This environmental surveillance data were compared to declared COVID-19cases at municipality level, revealing that members of the community were shedding SARS-CoV-2 RNA in their stool even before the first cases were reported by local or national authorities in many of the citieswhere wastewaters have been sampled.


It’s early days, but this sewage screening technology has been used to predict other viral outbreaks such as Norovirus and Hepatitis A and could give us some important insights into how widespread the virus is and where we might be about to see one of those already infamous spikes – allowing us to get ready to deal with it by changing rules and/or providing extra healthcare resources. In turn, this might limit the extent of the local outbreak.

(And it works the other way, too: we can note a decrease in wastewater virus levels and predict when to lift lockdowns appropriately.)

This isn’t a substitute for testing people, obviously. We don’t know whose poos we’re testing. But as a epidemiology management tool, it could be hugely useful. It should also assist when (if?) a vaccine for Covid-19 is rolled out, as general community prevalence of the virus will be a good indicator of both vaccine uptake and success.

The only downside is that someone has to wander around your local sewage farm, sucking up the effluent and testing it each day to get these numbers. So just thank your given deity that there are people willing (and possibly even excited) to do this work for the good of humanity.

Stay home. Stay safe. Poo regularly. Microbiology will do the rest.

Day 11 – pH

Some welcome rain yesterday. We still managed a day of fresh air and some exercise in the garden, but suddenly, Cape Town has gone all autumnal. Overnight.

Hopefully, it keeps people inside even more.

I got some useful advice on Covid-19 yesterday via the medium of WhatsApp, which might help you if you want to avoid the SARS-CoV-2 virus. [Spoiler: it’s terrible advice]

Damn that generally acidic virus! Combat it with well-known alkalis like… er… lemon and lime juice.
And damn that pH scale that only runs from 1-14.

“Sod that,” said the avocado farmers of South Africa. “We’re not going to be limited by your… your… ‘science’. We’re going all out for 15.6 – pushing the boundaries beyond the boundaries once again.”

Dandelions: “Hold my beer.”


Classic moments.


Countries in lockdown.
The 6 Nations postponed until October.
Curfews. Quarantine.
Stadiums empty for matches.
Toilet paper panic buying.
EU Parliament closed for “an unspecified length of time”.

It wasn’t great, but it was manageable.

Until this:

Awful news. Tragic.
And a real wake up call that we’re really not managing this whole pandemic thing very well at the moment.

Parliamentary suspensions, we could deal with. But no marmalade festival?

I’m done. Finished.