an autodidact meets a dilettante…

‘Rise above yourself and grasp the world’ Archimedes – attribution

the science of Covid-19: the virus, symptoms, spread, vaccine, incubation period, crude case fatalities

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So I’m now embarking on a series devoted entirely to the virus that’s shutting so many of us in our homes, feeling slightly (or considerably) fearful, for our lives as well as our livelihoods, feeling both frustrated and fascinated, both mystified and enlightened about human behaviour, governmental responses and the like.

First, some people call this virus Covid-19, some call it SARS-CoV-2, and most just call it coronavirus. But most well-informed people know by now that coronaviruses are quite commonplace RNA viruses (numbering in the hundreds). They’re relatively large and get their name from the corona or crown of proteins that spike out from the virus membrane. The official name of this new coronavirus is SARS-CoV-2 (that’s severe acute respiratory syndrome), and Covid-19 is the name of the disease or condition that the virus causes.

This is the third coronavirus in the last 20 years to infect large numbers of humans. Coronaviruses are zoonotic – they spread from animals to humans, becoming more potentially lethal in the process. The others were SARS in 2002 and MERS (Middle East respiratory syndrome) in 2012. The immediate species origin of this new strain is still unclear. According to leading epidemiologist Dr Edison Liu, sequencing has shown that it arose from a bat coronavirus, but it probably passed through a series of vectors before passing to humans. It appears to be less lethal than SARS or MERS, but its spread has been far more rapid. In an interview on the Jackson Laboratory website (JAX), Liu explains that the Covid-19 epidemic occurred at the same time as an influenza epidemic, and while the symptoms are very similar, Covid-19 has about ten times the mortality rate. The essential symptoms are fever, shortness of breath and coughing. Acute symptoms appear to result from a mix of direct viral damage and intense immunologic response in some cases.

The virus is spread primarily by coughing and sneezing, and from the time of contact with it until the time of symptoms is approximately four to seven days. The virus passes from the body in about 14 days on average – hence the recommended minimum quarantine period.

Liu had this to say about a vaccine. Vaccine development generally takes 12 to 18 months, not only to prove its efficacy but to scale up production to the required level. Animal models are needed to test the efficacy of any antiviral treatment. Covid-19 enters our cells through the ACE-2 receptor (angiotensin-converting enzyme 2). Mice, which are often used as test animals, don’t take up Covid-19 through their ACE-2 receptor, but scientists at Iowa University have developed an animal model for infection, in which the human ACE-2 receptor has been engineered into the animal (a mouse). So the effectiveness of antiviral drugs can be tested on these animals, which can apparently be provided en masse, with the Jackson Lab as a premier provider.

The invaluable worldometer website has regularly updated stats on total cases (about 1.1 million as of today, April 4), total deaths, total recovered, death rates and much else, as well as a country-by-country breakdown. It also has well-sourced and referenced info on symptoms, incubation period and other useful stuff. The incubation period is defined as the time from exposure to the development of symptoms. Worldometer sets this period as 2 to 14 days, according to data from WHO, China’s National Health Commission and the USA’s Center for Disease Control. Note that this period is longer than that stated earlier, in information from Jackson Laboratory CEO Edison Liu. Similarly a Chinese online community for physicians and healthcare workers has reported an incubation period of ‘3 to 7 days, up to 14 days’. However, rare outliers have been reported, with incubation periods up to 27 days. The WHO has considered these might be due to second exposures – incidentally raising the issue of re-infection. However, most experts feel that re-infection is unlikely, and this appears to have been borne out as the global spread advances.

Over the past day I’ve listened to two Sam Harris podcasts on Covid-19, interviews with experts conducted in early March – already long ago, it seems. The second, which I listened to first, was with Dr Amesh Adalja, of the Johns Hopkins Center for Health Security. He made an educated guess of the death rate for Covid-19 at 0.6%, based on his analysis of South Korean figures. This is approximately six times the rate for seasonal flu (though it should be mentioned that the most recent seasonal flu has been the most fatal for children in many years), but somewhat lower than many of the predictions of other experts. He also seemed, at that point, less concerned about the need for social distancing and other mitigating measures than others, but it seems that the rapid spread of the virus and growing public concern has rendered obsolete his nonchalance in this area. Also, stop press, a New Scientist article posted yesterday (April 3) has this to say on the South Korean data:

Crude case fatality rates are so-called because they don’t take into account the fact that some of the people counted in the infected numbers have not recovered yet and may still go on to die. Early in March, for instance, South Korea had a crude case fatality rate of just 0.6 per cent. That has risen to 1.7 per cent.

As to the fatality rate of Covid-19 at present, this is difficult to assess, largely due to ‘severity bias’, which means that many milder infections may be going untested, with only the more severe cases capturing the attention of the health care system, or even the infected. New Scientist reports ‘a wide range of estimates, from as low as 1 in 1000 to as high as 1 in 30’. It seems clear from current figures that death rates vary wildly from region to region, and country to country, but the reasons for this are still very unclear. To give some examples of the variation, the current crude case fatality rate for the UK is around 9%, for Italy it’s nearly 12%, but for Germany it’s only 1%. Here in Australia, it’s considerably less even than that, and no doubt governments around the country will be keen to take the credit. But there seems to be more to this variation than government action/inaction. This question along with many others will be explored in future posts.


Written by stewart henderson

April 4, 2020 at 4:01 pm

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