What SA’s Covid-19 data tells us: Infectious disease number-crunchers Low, Geffen

One of the positive stories amid the Covid-19 doom-and-gloom is that South Africa appears to be bearing up pretty well, with just over two-dozen deaths by the end of the long weekend compared to the staggering 11,000 in the UK and some 114 000 worldwide since the start of the year. Of the 2m cases worldwide that had been logged on the Johns Hopkins University website by Monday 13 April, just over 2,000 were reported in South Africa. But there's good reason for the government to maintain the strict lockdown measures, with data specialists urging citizens to treat the numbers with caution. In this podcast with BizNews editor-in-chief Alec Hogg, GroundUp editor Nathan Geffen and Spotlight editor Marcus Low – who have both pursued PhD studies on infectious disease modelling – explore some of the key areas where the data might not be reflecting an accurate picture. Geffen and Low have produced an in-depth piece dissecting the numbers and making sense of statistical headlines for those of us who are less numerate and are trying to understand the reach of the deadly Covid-19 virus in South Africa. – Jackie Cameron.Welcome to Marcus Low and Nathan Geffen, who have written an extraordinarily good piece. I say this because I've been asking many people in our country in South Africa how it is that the South African infection rates of Covid-19 are so low? Up until this morning I never got a straight answer. Just a little bit of background, Marcus what is your interest in this field?.___STEADY_PAYWALL___.I edit Spotlight which is a public interest health publication. We are a donor funded publication and our only goal is to increase public understanding of health issues, to make sure our government is held accountable for policy decisions around health and implementation around that. I'm also doing the PhD at University of Cape Town in computational modelling of infectious diseases, so all of this is right up my alley. I'm modeling tuberculosis which is where my interest is, but Covid-19 has overtaken all of that. .Nathan from your perspective, GroundUp is well-known, what is the purpose of the publication?.The idea is to publish news about human rights issues. Mostly published under Creative Commons license so that the bigger news publications like this can republish it. We try to focus on the stories that mainstream publications just don't have the resources anymore to go after, such as how various government policies are affecting people living in informal settlements and various vulnerable groups around the country..Your PhD was also in a very aligned area with the discussion today?.Yes, my PhD looked at computational modelling of the HIV epidemic. So indeed a confluence of unfortunate events has resulted in both Marcus and myself having a little bit of knowledge about this area. .Help rest of us, why are the numbers in South Africa so low?.The first thing to say is they might be low because they actually are low. The point of our article is to say that we don't know, there just isn't enough information in order to get a more definitive answer. The government is going to have to test a lot more people over the next few weeks and there is a plan to do that. There's a new test that's going to be implemented hopefully within the next week, using a device that's been used for TB testing up to now called the gen-expert. There are hundreds of these devices around the country, the government intends to use about 180 of them for testing for Covid-19. It just so happens that the company that developed this device has also managed to develop a test for Covid-19, originally it was for TB but now the machines are going to be repurposed for that over the next week or two now that Covid-19 has taken over. If that can be implemented and the amount of testing can be scaled up dramatically, we should get a better picture of the epidemic in South Africa. It's quite possible our numbers are low because we went into lockdown early, we took action early, 2 weeks before lockdown social distancing measures were introduced that might have worked. We don't know, and that that's the real point of the article, we just don't have enough information. .Marcus, the question that people are asking around the world is that flattening the curve is all very well but eventually people have to come out of lockdown and the theory is that most people in the population are going to contract this virus. In the South African context, is that something that is accurate or even relevant?.We don't really know yet, my best guess is that we probably will have to live with restrictions of some sort for many months at least. To bring it back to the testing question, the ability that we have to make informed decisions on whether we lift the lockdown or whether we keep this or that restriction in place, those decisions have to be informed by what we know, that's why testing is so important. I don't think we know whether we can safely lift the lockdown, we don't have enough information about what measures are needed. The forensic detail we have, the better positioned we will be to say, well, we need to keep economic activity going as far as possible, we can safely lift these restrictions..Nathan, the tests that you spoke about earlier, are they also going to be able to reflect antibodies? Given that the next big thing is if the people who've had a Covid-19 and have recovered and are not infectious. Maybe they could go back to keep the economic wheels turning?.The way the tests are currently done is we look for a specific part of the viral RNA or DNA, it's a long complicated story where we're looking for the virus itself. The gen-experts tests looks for the virus directly. An antibody test will look to see if your body has developed antibodies to fight against the virus. If you do have those antibodies then that means that you have at some point been infected by the virus but it doesn't tell us whether you're currently infected by the virus. The nice thing about our antibody test, when we eventually get them is that they're cheap and very quick, you can get a result within about 10 minutes. If you've ever gone for an HIV test you would know that that's how it works, you get your results within about 10-15 minutes because it's an antibody test. The problem now is if you do test antibody positive, another test would have to be done directly after looking to see if you're still infected with it or not. Another problem is that there are technical problems at the moment with the antibody tests that are being used in some countries. There was a write up in one of the world's leading medical journals the other day about this. I don't think we should get too excited at this point about antibody test, they are a while away, a month if not several months away. To make a point about our lack of knowledge, and yet that there are some things about this epidemic that we know a lot about compared to other epidemics. These days public opinion moves at the speed of Twitter, people want answers immediately to all sorts of complex questions. Unfortunately this epidemic is only a few months old. This virus didn't exist in humans until probably November/December last year and finance doesn't move as fast as people would like it to. That's just the way it is. At the same time, no epidemic in history, have we been able to within a few days or few weeks detect and sequence the genome of the virus. No epidemic in history after a few weeks of discovering its existence have we had a test for the virus. So it's incredible that the precedents that have been set are quite incredible. It took about three years from the discovery of AIDS to identify HIV as the cause. A disease was discovered that was killing people in America in 1981 and it wasn't until 1984 that the cause was identified. Here, we know the disease, the cause and you can go online to various websites and you can get updates every 20 or 30 minutes or so of the number of recorded cases and deaths around the world, it is incredible. So although there's a lot we don't know it's amazing how much we do know and how much we're learning and how quickly we're learning about it. We really are doing incredibly well considering, if you look back upon past epidemics, I suspect in the 1918 Spanish flu pandemic most towns that were hit by it didn't even know what was happening..Marcus from your perspective is a lockdown, a good or not a good thing? .In my view it's definitely the right thing, but it's a strange space as we're making our best guess decisions based on incomplete information. There is very compelling evidence from other countries that if you leave the virus to spread it can escalate very quickly with hospitals overrun with people and tough decisions have to be made about who gets ICU care etc. Based on the limited information we have I think it was the right decision, I don't know enough to say whether it should continue or what exactly the restriction should be after this. Just this question, on what we know and what we don't know, part of why we wrote the article was because we get these numbers every day, it's like watching for the latest cricket score. We want to know how many cases there are today and how many deaths, the point of our article is one of the things we've tried to do is to show that that's only a part of the picture and it's limited information that might be skewed in some kind of systematic way. One of the arguments we make is that instead of looking at all the cases simply as a single progression of 'this is how much the epidemic is growing', There's value in saying we had a lot of imported cases and the travel ban means that imported cases stopped, it could be one possible explanation of why the rates are going up so much. On the other hand we have local transmission that happens inside the country, which is the real fear. That might initially have been growing at a slower rate but in time can grow exponentially and overwhelm the healthcare system. The difficulty that comes with the shift from imported to local transmission is that three weeks ago it was really quite simple to say, if you recently traveled to Italy and you have symptoms you should get tested. We just don't have anything like that today. The symptoms are quite similar to many other things. So we're in this position now where we're not doing enough tests, it's very hard to know where to go for integrity tests. I guess the point was that those are plausible explanations for why they might be a lot more cases and we're not picking them up..If I understand it correctly we had this wave of imported cases and they're no longer being added to, what we now have to look at is the internal transmission and that might actually be at a very early stage of the exponential growth that we've seen elsewhere in the world..That's exactly it but hopefully the lockdown has to some extent slowed that local transmission. Based on what we've seen in other countries if we didn't have the lockdown I'd say there's a pretty high chance that we would have exponential growth, we don't know how effective the lockdown has been and how well people have adhered to it but the lockdown as a measure to prevent that rapid growth of the epidemic was definitely a reasonable decision..Nathan, what about the whole debate over BCG. The New York Institute of Technology correlation report that came out has not yet been peer reviewed; it's in the process of doing so which says that the TB vaccination which most South Africans have had can help in fighting off respiratory viruses. Is that something or are we clutching at straws here?.I suspect we may be clutching at straws. It's too early to be getting too excited about any vaccination that we might have had any particular treatments that are being pouted. There just isn't enough information and unfortunately medical science cannot move that cost. I would rather not venture an opinion on whether the BCG vaccination that most of us have had is going to have a protective benefit or not..How long is it going to take before we are in a position where we can start making decisions informed by data?.If the government can step up the testing massively and we can start getting a better picture of how many infections there are then we can start making more informed decisions. That's really key..I agree that that is absolutely the key. Testing is fundamental. The one thing I would add is that the government will be making very difficult decisions about what to do next. It's quite disappointing that we haven't really seen models published..Is there any good news or hope that you can share, given that you are very close to this subject?.With the caveat that we have incomplete knowledge, I'm reasonably confident that the lockdown and hopefully the two weeks of social distancing prior to the lockdown has slowed the epidemic. We haven't had reports of massive peaks in intensive care units. That suggests that the situation that occurred in Wuhan, Italy, Spain, America and increasingly in the UK hasn't happened yet. I don't want to say we are going to avoid it but it's not inevitable. With all the pain and suffering that the lockdown is no doubt causing millions of South Africans especially South Africans living in informal settlements, there are promising signs that it may be working that I don't want to overstate that because there just isn't enough information at this point..Marcus would you agree though that if we hadn't had social distancing and the lockdown that we might be in a very different situation in South Africa today..Everything indicates that. So far the measures we've taken have been reasonable and rational. We can't take that for granted. We have a history of AIDS denialism in this country. We know what it's like to have a government that does not understand or believe in the science. One reason for hope is that the president and the Health Minister have seemed willing to consult widely and to take decisions based on science, we hope that it continues in that way. We can't take that for granted. Making good policy at a national level is one thing and the Minister's leadership is definitely a positive sign, but a lot of the implementation happens in provinces and there we can run up against many of the well-known problems we have in our healthcare system and there's already been some shocking cases in Limpopo where the MDC for health is locking up doctors and isolating people in state facilities that could isolate at home. These things throw everything to undermine the actual implementation of what we do. It's worth keeping an eye on.

What SA’s Covid-19 data tells us: Infectious disease number-crunchers Low, Geffen

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