Important talking points on coronavirus COVID-19 pandemic

What is happening now? This is urgent and vital. Massive changes in social behaviour is necessary now now (in David Tribe’s considered personal opinion. 6 pm 22 March 2020.)

Australian numbers for daily new cases
The single most helpful real time graph: The deceleration detector:

Hopefully the turning tide will be confirmed over the coming days. There will be glitches though, due to mistake like the Sydney cruise ship release. But there are glimmers of hope

26 March 2020 7:30 data:

Tragically there is huge potential for increase in COVID-19 infection numbers in the coming weeks unless successful physical isolation is implemented widely. We shouldn’t expect this to work straight away but we might start seeing the impact in Australia by mid April.

Some idea of how much increase in numbers of infected people based on the assumption we have close to 200 undetected infections in addition to those that are being identified can be gained from looking at a recent Australian government document made available by the Prime Minister Scott Morrison.

This diagram below shows how infection spreads and how it’s affected by physical distancing and social isolation.

Without reading too much into the numbers they give some idea of how much increase in infection we can expect to see over the next 30 days either with or without effective physical isolation behaviours.

• Looking forward from a 23 March viewpoint we could see this:

Given this assumption that one person will affect 2 1/2 people in five days,  one undiscovered infected person circulating in the community can produce 406 cases in 30 days

If there were 200 people undetected but transmitting infectious today, they would generate 81,200+200 or approximately 82,000 cases in one months time

On the other hand with social distancing, meaning physical isolation people from one another, dramatically better results should be expected.

With physical isolation between people  the chances of exposure of others to infection can be reduced

Even 50% less transmission would result in 15+1 = 16 total infections in the community in 30 days time (as compared to 82,000).

Data here 

• Misinformation is dangerous. Make decisions based on advice from medically informed government agencies. University advice is generally reliable but health decisions need professional medical input. Other countries can provide important lessons.  This GMO Pundit blog is for general context only and not for personal medical decisions..

Source if not noted explicitly for Australia:
https://www.covid19data.com.au/

Relevant justification below.

Why you the reader should take the COVID-19 pandemic seriously?

The COVID-19 pandemic is much more dangerous than flu (impacting peak mortality with about 27-fold total lethality than flu (see * at the bottom of this page). This is because of a combination of newness to humans as it is a disease, with little existing immunity, high frequency of transmission of infection between people, high probability of serious disease outcomes, which increases with age, and lack of severe symptoms in many patients, allowing silent spread. At the start of the epidemic almost everyone in the world was susceptible meaning a surge in cases can easily overwhelm public and private health defences, inevitably leading to high death rates without timely preventative responses. A crucial shortage is lack of time since the epidemic starts with exponential growth, with infections doubling every 3 to 5 days, and we work largely in the dark about what has happened, finding out about infections about two weeks after they occur, and with these time lags, we don’t find out whether control measure are working for about two weeks into the future.

This is an existential threat to civilisation.

Numbers on the likely fatality rate are hard to estimate.A recent report 19 March in the Journal Nature Medicine says:

Using public and published information, we estimate that the overall symptomatic case fatality risk (the probability of dying after developing symptoms) of COVID-19 in Wuhan was 1.4% (0.9–2.1%), which is substantially lower than both the corresponding crude or naïve confirmed case fatality risk (2,169/48,557 = 4.5%) and the approximator1 of deaths/deaths + recoveries (2,169/2,169 + 17,572 = 11%) as of 29 February 2020

This is other vital information from the Wuhan outbreak paper just mentioned:

• In this graph, sCFR is the percentage of people with symptoms in different age groups that have died.
• Psym is the proportion of all infections yielding patients with symptoms. Susceptibility is the likelihood of infection. We are a bit unceratin about this number but this wont affct the main conclusions from this study.
• The clear message is that old people should stay home as they are more easily infected with symptoms, and the chances of them dying are greater.

Why you should take the information that’s at this page seriously?

The writer cares about the public getting accurate information about biology as this blog shows.There are perhaps one or two posts at this blog in about 4617 that the writer regrets.

David Tribe has been involved professionally in infectious disease since 1966 when he started as a cadet at the vaccine and blood products company CSL.
He has University training in chemistry, biochemistry, molecular biology and microbiology.
He has taught applied microbiology, bacterial genetics, food safety management, and risk management topics in a college teaching career spanning more than 45 years.

He manufactured vaccines at CSL in the 1970s. He worked in teams developing antiviral drugs and HIV testing technology at Dupont in the 1980s.  At the University of Melbourne in the 1990s he initiated research on insect virus molecular biology. He collaborated with the Microbiological Diagnostic Unit at the University of Melbourne to develop pathogen  molecular typing tools in the 2000s. He has published key papers and developed new tools to better manage the multiple drug-resistant pathogen Enterococcus faecium in hospital settings, that are highly cited by professionals.

Back to the epidemic.

• Common symptoms of COVID-19 infection include a fever and a dry cough (more details in graph below).

• Recent (March 17 data) from Italy at JAMA online show no cases in people under 30. Old people are severely at risk of death:

• There are several simple and effective tools to control the pandemic:

frequent and thorough washing of hands with soap and water, and physical  distancing. Disinfection of potentially contaminated surfaces touched by the public and use face-masks to protect others if you are unknowingly infected are other actions. If face masks are in short supply, their availability to medical professionals takes priority.

• It is important to act early to suppress the rate of exponential growth of cases at the start of the epidemic. Speed matters for several often difficult to explain reasons.

A New York Times article “The explosive power of now” brilliantly explains why. A diagram from this article captured below (as ” in the public interest” usage).

• Wonderfully well presented examples of where exponential growth of identified COVID 19 cases are at in Australia are provided at https://www.covid19data.com.au/ sample here:

• The point of infection controls, such as hand washing and social distancing, is to slow down the surge in cases so that the public health system is not overloaded with large case numbers. 

Overload would compromise effective treatment and necessary care for any patients who are in a critical situation.

• Concerted public action is especially important to protect vulnerable people such as the aged and those with existing conditions such as diabetes and heart conditions, who have a much higher risk of death from this disease.

• Control spread of infection by frequent and timely washing hands with soap and water and pay attention to washing completely all surfaces of the hands and lower wrist

Cough into your arm to minimise spread of droplets to surfaces near you and to other people.

Alcohol-based disinfectants are a practical alternative to soap and water, especially when moving around away from your home. Pure spirit should be diluted 3 parts spirit to one part water.

Common methylated spirits, called alcohol or ethanol by chemists, is suitable for disinfection use, but be aware that these spirits are inflammable.

Isopropyl alcohol is an alternative to alcohol, and should be diluted in a similar fashion.

Large gatherings such as fans attending a sports ground are an opportunity for repeated spread of infection.

The likelihood that at least one person is infected in a crowd increases with crowd size and so do the opportunities for infection transfer within the crowd. Simple math models with infected fraction and meeting size shown below guide policy decisions.

Trevor Bedford , @fredhutch on Twitter, 14 March 2020 estimated a rough level of 20,000 infections in the USA, with these doubling every 5 to 6 days. From this date and estimate we are within a week or so of infected people being almost certain to be present in crowds at large sporting events (see above diagram), a recipe for even more rapid increase in numbers of infections in the community.

Our World in data provides global coverage on numbers of COVID-19 patients that are identified (cases).

In addition to rapid spread and increases in numbers of infected persons, there are time lags and uncertainties in understanding the nature of the epidemic. These uncertainties make it difficult for specialists to understand the scope of the outbreak, as they cannot measure the actual current state of play.

It takes about a week or less between infection and symptoms to appear. During this time people may be infectious.

An authoritative report on the epidemic from Imperial College COVID-19 Response Team on 16 March 2020 London says this;

We assumed an incubation period of 5.1 days. Infectiousness is assumed to occur from 12 hours prior to the onset of symptoms for those that are symptomatic and from 4.6 days after infection in those that are asymptomatic …

It takes several weeks for people who are infected to die, so the statistics or death rates early the epidemic will have a downside error from this time-lag causing known infected people not being counted as a death because it will occur in the future.

Testing confined to people showing symptoms will not reveal many other symptom-free people who are still incubating the virus  and so the true extent of the epidemic will not be revealed by testing people with symptoms. As reagents for testing infection are in short supply, it is difficult to survey people who are not showing symptoms

This underestimation is compounded by the fact that the COVID-19 symptoms are quite commonly displayed in other well-known high prevalence diseases, such as colds and influenza.

In addition to the current state of play being hidden, the true severity of the epidemic and infection risk is not yet fully understood.

It certainly much worse than a common influenza epidemic, as it spreads very rapidly in a previously unexposed population, has a higher chance of producing extreme adverse consequences, including death, and there is little existing immunity to the virus to provide community protection.

The Italian tragedy.

*On 22 March 2020 the Italian mortality from COVID-19 peaked at 795 deaths a day (EU CDC data).
Combined with the known 2019 flu peak shown above of 29 deaths a day, suggests that the impact of COVID-19 is about 27-fold greater mortality than influenza.

It is clear that a significant fraction of hospitalised patients will require intensive care. Recovered patients may suffer permanent damage to their lung capacity