Saturday, March 28, 2020

debating the virus

Exponential growth

Eight days ago I sent some figures to a friend saying that if exponential growth continued, doubling every 4 days, then we would have 3,200 corona virus cases in Australia today (28/3)

Our government website, Coronavirus (COVID-19) current situation and case numbers, says that yesterday, 27/3 at 3pm there were 3,166 confirmed cases, so we are still on an exponential growth path.

From their graph the doubling looks roughly like this:

date   total cases
9/3        100
12/3       200
16/3       400
20/3       800
24/3      1600
28/3      3200

Extrapolating that further if the current exponential growth continues
1/4       6400
5/4      13,000
9/4      26,000
13/4     52,000
17/4    104,000
21/4    208,000
25/4    416,000
29/4    832,000

Nearly a million cases by the end of April. These figures, understanding exponential growth, explains the importance of an immediate lock down or hibernation.
Click on the image for a larger view. The lower reported figures in the last two days could be a positive sign or could be a delay in reporting.

update (new graph 4 days later, March 31st):
Hard to read at that size but click on the image for a larger view. Note that the reported figures for each day creep up after the day has passed. New cases on 26/3 are 280 on the first graph and jump to 360 on the second graph. New cases on 27/3 are 175 on the first graph and jump to 370 on the second graph.

Nevertheless, the curve has flattened a little. If doubling every 4 days had continued we would be up to 6,400 cases tomorrow (1/4) and our current figure of 4,359 (today, 31/3) is well below that.

The debate in Australia and world wide is divided between:
  • Those screaming for an immediate lockdown (#lockdownAustralia, Dr Greg Kelly) and critical of Scott Morrison for his ambivalence and mixed messages.

  • Those saying that the danger of this virus has been exaggerated, that the Infectious Fatality Rate is roughly 2 deaths in a 1000 cases (eg. Global Covid-19 Case Fatality Rates:
    Our current best assumption, as of the 22nd March, is the IFR is approximate 0.20%... and later .... Current data from Iceland suggests the IFR is somewhere between 0.05% and 0.14%
  • Those saying that it is more important to keep the economy going and that a lockdown will have worse consequences than attempting to contain the virus (eg. The Corona Dilemma)

  • Those saying that the capitalist system is inherently anarchic or unstable and that this event will push us into an economic downturn worse than the 1930s Depression (A Greater Depression?, People’s Forum: Economic Lessons for 2020)
My views:
I'll keep this brief since still reading and assessing:
(1) What should we do immediately? I agree with lockdown simply because there are empirical cases of
(a) it can overwhelm health systems as in Italy
(b) Some countries through lockdown have succeed in flattening the curve (China, South Korea, Japan, Hong Kong, Singapore)

(2) There is a lot we don't know about this particular virus, we need to learn a lot more. eg. as far as I'm aware we don't know whether young people with the virus who are asymptomatic pass it on to others. Of course there are a lot of experts working hard on this right now.

(3) What does the health endpoint look like and how long will that take? Can a vaccine be developed in less than 18 months? Apart from a vaccine what other end points are possible?

(4) Economic and political futures. The left has been lost for many years. There seem to be a few thinkers with a clue (eg. Michael Hudson, David Graeber) but no coherent movement to lead us out of this mess.

Tuesday, March 24, 2020

Second open letter from Australian doctors to Australian federal and state governments regarding COVID-19

Listen to this podcast interview of Dr Greg Kelly which explains the thinking behind the open letter in more detail.

Second open letter from Australian doctors to Australian federal and state governments supporting strong COVID-19 response to save the lives of Australians
To: Australian Prime Minister Hon. Scott Morrison MP
cc: Australian Health Minister Hon. Greg Hunt MP, Australian Chief Medical Officer Prof. Brendan Murphy, State Premiers and Health Ministers


Australian doctors, healthcare and emergency workers applaud the difficult decisions that have been made by governments this week alongside comprehensive economic measures. However, we are critically concerned that these measures remain inadequate to contain the transmission of COVID-19.

We support the immediate introduction of maximal measures. This means dramatic limitation of physical contact, by requiring all people to stay home, and a shutdown of all services that are not absolutely essential to provide for the necessities of life and functioning of the healthcare system.

We note that Australia is now an outlier amongst other nations that have moved to maximal shutdowns including the UK, New Zealand, Spain, France and Italy. These restrictions are inevitable, as at this stage of the pandemic they are the only way to avoid the disastrous loss of life and profound economic damage seen in Europe and the US. The demonstration of community transmission in NSW and Victoria now means that the virus has not and can not be contained. We need to urgently move to minimise the impact COVID-19 will have on the health system and our community. Despite efforts to increase the capacity of intensive care units across Australia, it is clear from international experience that a surge of critically ill COVID-19 patients can overwhelm even the best health systems and result in much higher death rates. We remain on track for this catastrophic outcome in Australia.

We explicitly endorse the Group of Eight advice of 22nd March commissioned by the Chief Medical Officer, that recommended a “go now, go hard, and go smart” strategy as the best way to “increase the likelihood of a speedier move to a national social and economic recovery phase.” While there will never be perfect information, the risk of further delays is simply too great to wait any longer.

We further explicitly endorse the call from the Australian Academy of Science that the data underpinning COVID-19 decisions in Australia be made public to enable scrutiny of key assumptions and input from frontline health care and emergency workers.

Finally, we are continuing to experience alarming shortages of personal protective equipment at the front line. This equipment is vital to protect the lives of healthcare and emergency workers and our families, as well as reduce transmission to the general community. We acknowledge government efforts in this area, but request urgent, ongoing attention to increasing supplies of personal protective equipment.

Tuesday 24th March 2020

Dear Prime Minister,

We, the undersigned Australian medical doctors, write again to express our grave concern regarding the rapidly escalating threat that Novel Coronavirus (COVID-19) poses to the lives of all Australians. We support the strong measures that Federal and State Governments have already taken to contain its threat and, additionally, support the even stronger measures that we know will be required in the days ahead.

We request:
1. The immediate shutdown of all non-essential services in Australia and strict social isolation to limit the spread of COVID-19;
2. Continued strong support for health systems to prepare to face a surge of COVID-19 patients; and
3. Further attention to the risks for Indigenous, rural and remote Australians.

Each of these points is addressed in more detail below.

When 7,000 Australian doctors wrote to you on the 17th of March we made alarming predictions regarding the rate of increase of COVID-19 infections in Australia that have since proved conservative. Worryingly, our prediction of 1,500 cases by today was realised a day early. Italy has continued to suffer very high mortality rates and other developed countries including the United Kingdom, United States, Spain and France are all now suffering from hundreds of deaths as severe COVID-19 cases overwhelm their health systems. We are very concerned that Australia, with 1,700 cases but thankfully few deaths, is currently in a similar situation to the UK's of 14 March, when they had 1,100 cases and 21 deaths. Now, as you know, the UK has had 5,500 cases and 280 deaths. Given our current rate of case increases and the fact that it takes infected patients some time to develop critical illness, we are very concerned that we are little more than one week from a comparable situation. We commend that Australia has performed more COVID-19 testing than most other countries and that faster testing kits are arriving, however, this does not change the current numbers nor the trajectory. Hence, the time to act is now.

We appreciate that Federal and State Governments are giving the situation their full attention and resources, and attempting to balance health risks against severe social and economic ones. We applaud the measures that you and State Premiers have announced in recent days in suspending non-essential gatherings, and note that further measures have been flagged. However, we are concerned that these measures are not being implemented soon enough to slow or halt transmission. Therefore, we support immediate, further action, including a national shutdown of non-essential services and enforcement of strict social distancing. Although these measures will be challenging for us all, implementation needs to happen now to give Australia the best chance to minimise the human and economic toll from this disaster.

Last week, we requested that our health systems urgently prepare for a surge of COVID-19 patients. We appreciate the leadership and resources that have been dedicated to this issue in the last week. Healthcare workers and systems are now clearly focusing on these preparations. However, we need more time and resources at the front-line. Preparations remain incomplete. These include obtaining adequate supplies of personal protective equipment (PPE), training to use it properly and environmental changes to minimise the risk to staff from COVID-19. Also, measures to increase our capacity to care for critically ill patients are lagging - many hospitals are still performing elective surgery, repurposing of areas remains incomplete and vital equipment has yet to arrive. We need more time for this preparation. Hence, reducing the rate of COVID-19 transmission remains critically important. Recent experience from Italy shows that poorly-protected healthcare workers are at substantial risk from COVID-19. It also shows that the mortality rate from COVID-19 can be as high as 4% when health systems are overwhelmed, compared to 1% when they are not.

Finally, we appreciate the attention that has so far been paid to ensuring the health of Indigenous, rural and remote Australians in this crisis. We support ongoing measures to limit transmission in these areas, build capacity and support Indigenous, rural and remote health workers and healthcare.

With these strong, immediate measures, Australian doctors stand ready with their communities to face COVID-19. We cannot do this alone. We need the help and support of the Australian people, and of our representatives in government, to give us the best chance of saving the lives of your loved ones and to protect ourselves and our families too.

Yours sincerely

Sunday, March 22, 2020

5 countries have flattened the corona virus curve

Click the image for an enlarged view.

This graph shows which countries have developed effective measures and have flattened the curve (South Korea, Japan, Singapore, Hong Kong, China) and summarises how they did it.

On the other hand the USA has the sharpest upward trajectory.

Note that the vertical axis is logarithmic not linear.

The best information I am obtaining comes from Dr Greg Kelly's twitter feed

For Northern Territory vital corona virus updates follow Dr John Boffa's twitter feed

Great news!:
Northern Territory introduces strict new coronavirus border controls to halt COVID-19 spread
The Northern Territory will introduce strict border controls from 4:00pm on March 24 that mean anyone arriving from interstate or overseas will have to self-isolate for 14 days.

Key Points:
  • Restrictions will not halt the delivery of essential goods and services
  • There are some exemptions, including health services and police
  • The measures are likely to remain in place for six months
Chief Minister Michael Gunner announced the new restrictions on Saturday

Tuesday, March 17, 2020

Open letter from Australian doctors to Australian federal and state governments re. coronavirus COVID19 emergency response

This letter was initiated by Dr Greg Kelly (his twitter feed)

Open letter from Australian doctors to Australian federal and state governments re. coronavirus COVID19 emergency response
To: Australian Prime Minster Hon. Scott Morrison MP
CC: Australian Health Minster Hon Greg Hunt MP, Australian Chief Medical Officer Dr Brendan Murphy, State Premiers and Health Ministers

Monday 16th March 2020

Dear Prime Minister

We, the undersigned Australian medical doctors, are writing to you today because of our grave concern regarding the threat that novel Coronavirus 19 (COVID19) represents to the lives of Australians. We believe that Australian federal and state governments can avert disaster by heeding the lessons of other countries.

This means:

1. Immediately implementing the strict measures of lockdown and social distancing that have been shown to be effective at slowing the spread of COVID19 and,
2. Preparing our health systems for a surge of COVID19 and critically ill patients.

Taken together, these measures would reduce the numbers and presentation rate of COVID19 patients and allow our health system to cope.

International experience is that the COVID19 virus behaves in a relatively predictable way with the number of cases doubling every 3-5 days before strict lockdown and social distancing measures are implemented. Data from China, Europe and now Australia support this assertion. Exponential growth of this kind leads to relatively small numbers of infected patients to become large numbers at first slowly and then very, very quickly.

On current growth rates the 370 cases in Australia today will be 750 on Friday, 1500 on Tuesday next week, 3000 next Saturday, 6000 on the 1st of April and 12 000 by the 4th of April. This is less than 3 weeks from now and puts us in a worse position than Italy is currently in. Experience from China and Italy has also shown us that social distancing changes implemented today will take 2 weeks to show an effect on the numbers of diagnosed new cases due to the lag between initial contact and development of severe disease. We are especially concerned about impacts on Indigenous communities given their high rates of pre-existing illnesses and limited health infrastructure.

While we applaud the measures that have been taken by Australian authorities so far we know that they are not enough. The Italian government believed that they were acting decisively with their first local lockdowns at just 21 confirmed national cases, far lower than the current rates in Australia. Many of us are in contact with colleagues in Italy, Spain and France and they are begging us to learn from their mistakes.

The Italian authorities are reporting much higher rates of critical illness in their population than reported in Wuhan, China. This is likely related to an older population demographic with more pre existing illnesses. Australia is much more similar to Italy than Wuhan in this respect. Patients with critical COVID19 illness require admission to an intensive care unit for respiratory support and require highly specialised staff, equipment and locations, all scarce resources that cannot be easily increased. The Italian region of Lombardy which is currently hardest hit by COVID19, is one of the richest areas in Europe with a health system equal to that of Australia's. Our colleagues there have made herculean efforts to increase their capacity to care for critically ill COVID19 patients. Despite their efforts their systems are completely overwhelmed with corresponding very high death rates and inability to provide intensive care to previously healthy seventy year olds. They describe their situation as like being "in a war zone." With access to intensive care the death rate from COVID19 is likely less than 1%, but in an overwhelmed system without access to intensive care the death rate approaches 4%. Today, Italy has reported over 2100 deaths.

Fortunately, experience shows that COVID19 transmission rates can be significantly reduced if we heed the lessons of other countries. Chinese provinces outside Wuhan are excellent examples of this, as are Singapore, Korea and Taiwan. Widespread economic lockdown and social distancing are what is required. Transmission still occurs but the number of severely ill people remains within the capacity of our health system to treat them. The international experience has been that this decision cannot be averted, only delayed, and that the cost of delay in economic and human terms is higher than the cost of acting early and decisively. Furthermore, due to their experience with SARS, countries like Singapore can teach us valuable lessons about minimising economic effects from such epidemics.

Our second request is that urgent preparations are made to prepare our health systems for an unprecedented surge of COVID19 infected and critically ill patients. Such measures include an immediate reduction in elective work, increased frequency and intensity of hospital cleaning, measures to temporarily increase intensive care capacity and increasing personal protective equipment for staff.

With these immediate measures, Australian doctors and health care workers stand ready with their communities to face COVID19.


Related: Covid_19: Open letter from Italy to the international scientific community

As you surely know, Italy is suffering a dramatic spreading of the coronavirus.

In just 3 weeks from the beginning of the outbreak, the virus has reached more than 10.000 infected people.

From our data, about 10% of patients require ICU (Intensive Care Unit) or sub ICU assistance and about 5% of patients die.

We are now in the tragic situation that the most efficient health system of the richest area of the country (Lombardy) is almost at its full capacity and will soon be difficult to assist more people with Covid-19.

This is the reason why an almost complete lockdown of the country has been ordered: to slow down and hopefully stop the contagion as soon as possible.

The virus is spreading at maximum speed, doubling the number of infected people in just 2,4 days[1].

As it emerges without a doubt from the data available, all the European countries are in fact experiencing the same rate of contagion speed and that they are just a few days behind on where it is Italy now [2].

The beginning of the outbreak had the exact same number of infections in China, Italy, and other countries. The difference is that China strongly and quickly locked down Wuhan and all of the Hubei region 8 days before Italy [3].

Just 8 days of delay for the Italy lockdown will result in an enormous increase in the number of total deaths in Italy with respect to China.

This exact same initial dynamic in the number of new cases can also be observed in every country outbreak.

It’s hard for non-specialists to intuitively grasp the way an exponential rate increase can get out of control.

So it’s very difficult to realize the tragic consequences that an exponential growth can have in a contagion like this one.

As a scientist, you surely do understand it. You do also understand that, as long as the rate of increase is exponential, no linear solution to contrast it will work (I.e. increasing x times the number of ICU machines, etc.)

Similarly, just imposing a limitation on people from staying together in large groups is not a sufficient solution.

This is an appeal to you, as a member of the scientific community, to urge your government to act now for actively stopping the virus!

In most EU countries you have enough time to make a lockdown similar to China or South Korea to quickly slow down and stop the contagion with much less effort and cost of what is now needed in Italy.

If Italy had strongly acted just 10 days ago, and that is more or less where you are now, there would have been much fewer deaths and economic tumble.

South Korea and China should be taken as the example to follow to stop this epidemic.

There is no other way.

So please, make your best effort to urge your government to act now! Time is our common enemy as the virus is very fast and really lethal.

Every minute is exceptionally important as it means saving lives. Don’t waste it!

Take care.

Monday, March 16, 2020

Report of the WHO-China Joint Mission on Coronavirus Disease (summary)

Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19) (Feb 10- Feb 24, 2020)

I've extracted some of the main points. The whole report is 40pp.

Zoonotic origins
COVID-19 is a zoonotic virus. From phylogenetics analyses undertaken with available full genome sequences, bats appear to be the reservoir of COVID-19 virus, but the intermediate host(s) has not yet been identified

Routes of transmission
COVID-19 is transmitted via droplets and fomites (eg. human skin cells, hair, clothes, bedding) during close unprotected contact between an infector and infectee. Airborne spread has not been reported for COVID-19 and it is not believed to be a major driver of transmission based on available evidence

Household transmission
In China, human-to-human transmission of the COVID-19 virus is largely occurring in families. … Among 344 clusters involving 1308 cases (out of a total 1836 cases reported) in Guangdong Province and Sichuan Province, most clusters (78%-85%) have occurred in families.

Contact Tracing
China has a policy of meticulous case and contact identification for COVID-19. For example, in Wuhan more than 1800 teams of epidemiologists, with a minimum of 5 people/team, are tracing tens of thousands of contacts a day.

Transmission in China outside of Hubei
To date, most of the recorded cases were imported from or had direct links to Wuhan/Hubei. Community transmission has been very limited. Most locally generated cases have been clustered, the majority of which have occurred in households, as summarized above.

Data on individuals aged 18 years old and under suggest that there is a relatively low attack rate in this age group (2.4% of all reported cases).

The signs, symptoms, disease progression and severity
Symptoms of COVID-19 are non-specific and the disease presentation can range from no symptoms (asymptomatic) to severe pneumonia and death. As of 20 February 2020 and based on 55924 laboratory confirmed cases, typical signs and symptoms include: fever (87.9%), dry cough (67.7%), fatigue (38.1%), sputum production (33.4%), shortness of breath (18.6%), sore throat (13.9%), headache (13.6%), myalgia or arthralgia (14.8%), chills (11.4%), nausea or vomiting (5.0%), nasal congestion (4.8%), diarrhea (3.7%), and hemoptysis (0.9%), and conjunctival congestion (0.8%).

People with COVID-19 generally develop signs and symptoms, including mild respiratory symptoms and fever, on an average of 5-6 days after infection (mean incubation period 5-6 days, range 1-14 days).

Most people infected with COVID-19 virus have mild disease and recover. Approximately 80% of laboratory confirmed patients have had mild to moderate disease, which includes non-pneumonia and pneumonia cases, 13.8% have severe disease ... and 6.1% are critical (respiratory failure, septic shock, and/or multiple organ dysfunction/failure).

Individuals at highest risk for severe disease and death include people aged over 60 years and those with underlying conditions such as hypertension, diabetes, cardiovascular disease, chronic respiratory disease and cancer. Disease in children appears to be relatively rare and mild with approximately 2.4% of the total reported cases reported amongst individuals aged under 19 years. A very small proportion of those aged under 19 years have developed severe (2.5%) or critical disease (0.2%).

Mortality increases with age, with the highest mortality among people over 80 years of age (crude fatality ratio, CFR 21.9%)

While patients who reported no comorbid conditions had a CFR of 1.4%, patients with comorbid conditions had much higher rates: 13.2% for those with cardiovascular disease, 9.2% for diabetes, 8.4% for hypertension, 8.0% for chronic respiratory disease, and 7.6% for cancer.

Knowledge gaps
Annex D summarizes the key unknowns in a number of areas including the source of infection, pathogenesis and virulence of the virus, transmissibility, risk factors for infection and disease progression, surveillance, diagnostics, clinical management of severe and critically ill patients, and the effectiveness of prevention and control measures. The timely filling of these knowledge gaps is imperative to enhance control strategies.

Much of the global community is not yet ready, in mindset and materially, to implement the measures that have been employed to contain COVID-19 in China. These are the only measures that are currently proven to interrupt or minimize transmission chains in humans. Fundamental to these measures is extremely proactive surveillance to immediately detect cases, very rapid diagnosis and immediate case isolation, rigorous tracking and quarantine of close contacts, and an exceptionally high degree of population understanding and acceptance of these measures.

For the public
1. Recognize that COVID-19 is a new and concerning disease, but that outbreaks can managed with the right response and that the vast majority of infected people will recover;

2. Begin now to adopt and rigorously practice the most important preventive measures for COVID-19 by frequent hand washing and always covering your mouth and nose when sneezing or coughing;

3. Continually update yourself on COVID-19 and its signs and symptoms (i.e. fever and dry cough), because the strategies and response activities will constantly improve as new information on this disease is accumulating every day; and

4. Be prepared to actively support a response to COVID-19 in a variety of ways, including the adoption of more stringent ‘social distancing’ practices and helping the high-risk elderly population.

Friday, March 06, 2020

useful articles about the corona virus

update: (March 13th)

It is easy to overdo COVID-19 quarantines

This one covers the nature of the virus, the health and economic issues.

Quarantines and restricting events with huge crowds (Scott Morrison's current "solution") will slow down the spread of the virus but won't stop it. It is unlikely that a vaccine will be developed soon. So, the virus will continue to spread to a large percentage of the population. This will lead to a profound economic downturn.

On a personal note, wrt health issues probably the smart thing for an elderly person like myself to do is take supplements to improve my immune system:
Nutrition experts recommend supplementing diets with Vitamins A, C, E, antioxidants and selenium. Other experts say zinc, Vitamin D and elderberry may be helpful
How does the coronavirus outbreak end?

Deaths by age in mainland China:
over 50: 94%;
under 50: 6%
You’re likely to get the coronavirus.

The assertion was based off an estimate from Harvard epidemiologist Marc Lipsitch, who predicted some 40 to 70 percent of all adults around the world would catch the virus within a year. Lipsitch has since revised that estimate downward and with a greater range: He now estimates it’s “plausible” that 20 to 60 percent of adults will catch the disease. (If this comes to pass, while being bad, it’s not apocalyptic: Most cases of Covid-19. are mild. But it does mean millions could die.)

In an email, Lipsitch says his model “assumes that the transmission in the rest of the world is at least fairly similar to that in China.” But “projections should be made with humility,” he adds, as there’s a lot still to uncover that will impact the forecast (like the role children play in spreading the disease).
Did the coronavirus get more deadly? The death rate, explained

From the figures it appears that the death rate from those infected is 3 to 4%. But this is misleading because many mild cases are not reported.

Worldometer corona virus

The latest stats: The coronavirus COVID-19 is affecting 124 countries and territories around the world (March 12, this figure increases daily)

Original post (March 6th) At this point I'm persuaded it will lead to a global recession. The first article talks about this and I can't refute it.

The second article is about overlooked issues, quite interesting. The third one is about how our health systems are susceptible to hacking.

The Gathering Storm: Could Covid-19 Overwhelm Us in the Months Ahead?

Easily overlooked issues regarding COVID-19

Security of Health Information