Day 106 – No definite answer

It’s cold, grey and wet. We’re sheltering behind closed curtains and in front of a fire, either working on spreadsheets, working on school stuff or reading sobering, cautionary correspondence about how we, as the human race, are going to deal with the SARS-CoV-2 virus.

The widespread opinion has been that we’re in this sticky situation until we can get a vaccine sorted, rolled out and administered to as many people as possible. And that’s the goal.

But there are signs that it’s not going to be quite as simple as Design Vaccine, Mass Produce Vaccine, Immunise World Population. Never mind the clear difficulties inherent in steps 2 and 3: number 1 seems to be proving more problematic than we had hoped.

This BMJ editorial from various UK academics spells out (some of?) the potential problems with any vaccine (and other immunological therapies) for Covid-19

Worldwide, many covid-19 vaccines are at various phases of development…
Understandably, there is great public expectation that these efforts will be successful, but caution is necessary with respect to both vaccines and passive immunity.

Vaccine being poking you with stuff that will make your body produce antibodies against Covid-19, and passive immunity being short-term protection by poking you with ready-made antibodies taken from someone who has had Covid-19.

Both are good ways to prevent people getting any given disease, but there are no guarantees that either of them will be successful against Covid-19.

There are many reasons why they might not work, or why they might not work as well as we would like or need them to:
Vaccines don’t work as well in older people: Covid-19 disproportionately affects older people. So can we make it work in the people that need it most?
The bit of the virus that we are hoping to target with the vaccine might mutate – meaning that even if we make a working vaccine, it might not work for very long.
We’ve never managed to make a vaccine against SARS or MERS – both very similar viruses to this nasty bugger – despite years of trying.

And – it’s complicated – but giving antibodies to patients might not be the best plan either. It’s worked well before with other diseases (even Ebola!), but this isn’t other diseases. In fact, there’s even the risk that – because of the way some cases of Covid-19 progress – giving convalescent serum (the antibodies) to a patient might even make them sicker.

Finding the solutions to these problems isn’t something that you or I can influence, but I just felt that it was worth putting it out there that you should probably abandon those foregone conclusions that science will have this all sorted out by Christmas (or whenever).

Sorry about that.

Day 102 – Virus FAQs

I’m still being asked a lot of questions about the virus situation here in SA. Microbiology is my passion and I’m happy to be asked, happy to answer. But maybe I can save us all some time and effort by answering some of the more commonly asked questions on here.

I’m not saying that this is the only way to do things, or necessarily even the best way of doing things: everyone will have their own approach and that’s fine. But this is the way we’re doing things, based on science, our knowledge and the changing situation around us. And yes, things are constantly changing, so it’s therefore reasonable to assume that our approach will change when required as well.

You’ll notice a common theme, one that I have eluded to many times before: it’s all just one risk individual assessment after another. Basically: how much do I need to do this and how much risk is there of me getting the virus from doing it?

Where you can, avoid risky situations: close proximity to others, indoor spaces – especially poorly ventilated indoor spaces and especially spending a prolonged length of time in those sorts of spaces. Apply that approach to your daily life (it’s really not as arduous as you might think) and generally you’ll end up doing things right.

Questions.

Are we in the clear in Cape Town now? 
No. We’re not. The focus over the last couple of weeks has definitely moved to Gauteng, but this isn’t a light switch. You don’t just flick one place on and another goes off (and actually, that’s not even how light switches work, is it?). The situation in Cape Town still awful and no, you shouldn’t let your guard down. Right now, wherever you are in the country, it’s safest to assume that the virus is everywhere and alter your behaviour accordingly.

Should I be wearing a mask?
Yes. Wearing a mask is cheap, easy and has huge benefits, especially for those around you in that it limits the distance that any virus you breathe out, can go. And sure, I know that you don’t have the virus, but science has shown that asymptomatic transmission (passing the virus on even though you don’t feel ill) is a huge factor in the spread of Covid-19.
There is no downside to wearing a mask.
The Disaster Regulations say you must wear a mask when you are in a public place. And good luck with getting into any private establishment (shops, restaurants etc) without wearing one.

Should I be shopping?
Not unless you need to. Certainly not for pleasure. Shops are generally indoor spaces and you really should be avoiding those wherever you can. If you can order online, do so. If you can’t, then get in and get out as quickly as possible. Groceries are one thing, but I promise that you really don’t need to get those shoes or buy that new vase right now. Do that quick mental assessment: the risk is likely the same for grocery shopping and shoe/vase shopping, but only one is necessary. See how easy this is?

Should I be going to bars and restaurants?
In my humble opinion: hell no. Just because these places are open for business, doesn’t mean it’s a good idea to go there. People with masks off (for eating and drinking), inside space, prolonged period of time, and often speaking loudly because of background noise/music. These are all high risk behaviours/situations. Put them all together and it’s a recipe for disaster. By all means support your local restaurants, but do it via delivery or pick-up.
Sit down meals are not a good idea right now. Sit down meals are actually a very bad idea right now.

Don’t we all?

And haircuts?
I would love to have a haircut. But again: just look at how you have a haircut: someone stands right next to you (right over you, even) in a small space for a good length of time. This is not a safe situation. This is an easy call. And it’s a strong no from me right now.

Cinemas, theatres and casinos?
No: Indoors. Proximity to other people. Prolonged duration of potential exposure. Ticking lots of those High Risk boxes and none of the Absolutely Necessary ones. Red flags everywhere.

Is meeting friends ok?
Difficult one. There’s more to life than physical health. Mental health is hugely important too, and we all require some degree of social contact to keep us sane. Zoom calls can only go so far to satisfy this need. So let’s put this in perspective: while not meeting friends poses zero risk of infection, meeting friends carefully, in controlled conditions: socially distanced, with masks on and OUTSIDE poses very limited risk of infection.

Here’s something else to factor into your quick risk assessment. It’s Dr Everett Koop’s quote:

When you have sex with someone, you are having sex with everyone they have had sex with for the last ten years, and everyone they and their partners have had sex with for the last ten years.

Now, I’m not suggesting that you have sex with your friends – that’s your call (and theirs, obviously). But with a little tweaking, that quote reads like this:

When you meet a friend, you are meeting everyone that they have met with for the last fourteen days, and everyone that they and their family have met in the last fourteen days.

How sensibly have your friends (and their families) been behaving?

Should I meet elderly/vulnerable friends or family? 
Hard no. As difficult as this may be, it’s going to be a whole lot more difficult when they contract the virus and get sick or die. No good can come of them spending time with anyone at the moment. Horrible situation, I agree. Nothing we can do about it. Sorry.

Any quick advice for me?
Wear a mask (limits risk of transmitting virus).
Wash your hands often (removes any virus from your hands before it can get inside you).
Stay at home as much as you possibly can (the virus can’t come to you – you must go to it).
Don’t go into indoor spaces with other people where you can possibly avoid it (this is a high risk activity).
Remember that time is important (the longer you stay in any risky situation, the more chance you have of being infected).

There you have it. I’ve avoided the thorny “Should my kids be going to school?” one, because there are just too many variables and too much emotional stuff there. That’s even more of an individual choice than anything else here.

As mentioned above, I’m not saying that these answers are right for everyone, but I believe that the thinking and the approach behind them is solid and is a good way for anyone to gauge whether you should be taking part in any given activity.

Stay home. Stay safe. Have a great day.

Day 100 – Searching for the silver lining

It’s 100 days since SA locked down. In that time, we’ve done the hard yards of Level 5, the only-ever-so-mildly-easier yards of Level 4* and then slipped into the sloppiness that is Level 3 (and then “Advanced Level 3” – which nobody quite understands).

Cigarette sales are still bizarrely banned, but other than that, life is going on pretty much as usual, albeit (mostly) with masks.
That and, oh yes, the virus being more prevalent and deadly than ever before.

Much has been made of England’s decision to reopen pubs and restaurants this week, but that’s an example of one of the “impossible” choices that Governments have had to make when balancing infection rates and jobs (in this case in the remnants of the hospitality industry). Those individuals whinging and whining on social media about how it’s “too soon” and “too dangerous” may have a point, but also clearly have no concerns about the close on a million jobs in pubs, restaurants and hotels in the South East of England alone. And yes, there will be spikes in infections as people start to interact more normally again, but we’re going to see spikes all over the world for (probably) years to come. We cannot wait for a the chance of a vaccine before we start to open our economies again.

In fact, South Africa didn’t even have the luxury of waiting until the infection rate began to level out. Our fragile economy meant that the lockdown had to be relaxed right as the virus started to take hold: a perfect storm of natural infection and enhanced movement and social interaction, all in one. Wonderful.

And it is still going to get (much) worse here before it starts to get any better.

It’s easy (and natural) to look at the past 100 days and see the despair, the disasters and the difficulties. It’s been a truly horrendous few months. And – perhaps because it’s such low-hanging fruit – everyone has done it. Regularly. Often. I are also guilty.

So, with 100 days chalked up on the cell wall, I wondered about looking for any positives that have come out of the situation. I’ll start by warning you that there aren’t many, but that doesn’t mean that they should be overlooked. There may be a lot of clouds, but some of them must have silver linings, right?

The enhanced sense of community is something that I have noticed. The acceptance that this situation is bigger than any of us, and that we need to work together to help one another. From friendly tips and offers to help on the local Whatsapp groups, through charities benefitting from people having more time to assist, to a greater appreciation of those services and individuals who have been working to keep things going – as much as has been possible – throughout.

Peace and quiet: fewer cars on the road and an overnight curfew meant that we could hear birdsong during the day and the Spotted Eagle Owls in the darkness. Caracals didn’t get killed on our roads, penguins took over Simonstown. Dolphins returned to Table Mountain.

THERE WERE NO TOURIST HELICOPTERS FLYING OVER MY HOUSE EVERY TEN MINUTES AND IT WAS GREAT!

Seriously, check the carbon footprint on that particular experience, guys.
And then stop it. Permanently.

Family time. Forced to spend time together, we… actually spent time together. We played games together, we exercised together (sometimes in the living room, sometimes in the garden, sometimes (when we were allowed) in the real world! We even spent (online) time with other families, doing stuff like quizzes and virtual evenings out.

We had to find new ways to work: restaurants did deliveries, supermarket apps upped their lousy game to be slightly less lousy, we supported local businesses and stores where we could. Not carrying your laptop to a different desk on the other side of the city each morning and then back again each evening became a thing. (Some) schools successfully managed to teach their students. Technological progress was fast-tracked and shaky, but (mostly) held together.

I understand that these positives don’t outweigh the huge negatives which the country has had to endure, and also that for many people, there has been no bright side at all. We’ve been lucky in that we have the means – and the space – to generally handle what this situation has thrown at us so far.

But that doesn’t mean that we shouldn’t try look for the good bits of what has happened over this last 100 days: this whole state of affairs is overtly negative, and will quickly drag you down unless you cling to the occasional positive. So that’s what I’ve tried to do here.

I’ve decided that The Lockdown Diaries posts will continue for the moment – at least until life returns to normal. (lol!)

That might be a while yet, but together, somehow, I’m confident that we’ll make it.

 

* there was still no alcohol

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.

Phew.

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.

Wow.

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 96 – An expert speaks

Let’s (not) lighten the mood with this little gem from the Daily Maverick webinar yesterday, shall we?

Here’s a rather grim warning from Prof. Shabir Madhi, member of SA’s scientific advisory council:

People are getting infected at a phenomenally high rate. It’s unbelievable. Not in my wildest imagination did I think people would get infected as much as they’re getting infected right now. What you’re going to see in Gauteng in the next three or four weeks is going to be really frightening.

When scientists and professionals use language like that, you know that things have got a little bit out of hand. He continues:

The number of people we’re diagnosing on a daily basis, which is still a fraction of the true number of people infected, is absolutely frightening.
They’ll all end up in hospitals in 2 to 3 weeks from now.

In Gauteng, like many other places in SA, people are not avoiding crowded spaces, they’re not wearing face masks, they’re not ensuring physical distancing. That has fuelled the transmission of the virus.

Yep: Gauteng is the new Cape Town.

And while just a few weeks ago, they were laughing at us and calling us “Western Cape Wuhan”, they’re now dying in their droves.

Who could have seen that coming?

The rapidly opening economy, now including restaurants, cinemas, casinos and “personal care salons” flies in the face of pleas from the Health Department for people to stay at home. I’m sure that we’ll see spikes all over the country from this, though in the case of Gauteng and the Eastern Cape, they might be well hidden behind the exponential increases there anyway. The bigger worry for the Western Cape now is surely that people think it’s all over and give up any attempt to protect themselves or others.

Spoiler: This is not all over.

Because, as you can read above, even during the worst of it, the number of people choosing not to socially-distance or cover their noses and mouths while out and about, flies in the masked faces of the advice from the experts.

I have no answers. No ways to solve this. We’ve been through it so many times on here. Quite how much more the government can do to communicate the simple steps to reduce the risk of transmitting and contracting Covid-19 is beyond me.

For more and more people, it’s now just getting to the point of protecting themselves and their own families. Only go out and about if you really need to* – especially to anywhere indoors (good practical advice here, remember), because people are going to break the rules, they aren’t going to wear masks and they will come too close to you:

Don’t blame a clown for acting like a clown, blame yourself for going to the circus.

Although I’m very happy to blame the clowns as well.

 

* I don’t count casinos, hairdressers, cinemas and restaurants in this category (sorry Corné).