Flattening the Coronavirus curve

Most European governments completely misread the epidemic although they had time to learn from the Chinese experience.
First they misunderstood exponentials, (it starts slowly then goes up fast) and did nothing. Then they over-reacted looking at models saying half the population would get sick with 3% dying and finally settled on the only option left: "Flatten the curve!" The result is that in a month or two, a large chunk of the economy will be gone. There will be hell to pay. Confinement and the dictatorial measures which come together will not be tolerated very long in many countries. The 4th turning is upon us!

But for now, that is indeed the only option left. 
Here is a good brief
https://phys.org/news/2020-03-endgame-restart-coronavirus.html
Here is the complete original statistical work from the Imperial College in London:
(The link seems to be broken so I insert a copy of the summary, pdf below)

Impact of non-pharmaceutical interventions (NPIs) to reduce COVID-19 mortality and healthcare demand

Neil M Ferguson, Daniel Laydon, Gemma Nedjati-Gilani, Natsuko Imai, Kylie Ainslie, Marc Baguelin, Sangeeta Bhatia, Adhiratha Boonyasiri, Zulma Cucunubá, Gina Cuomo-Dannenburg, Amy Dighe, Ilaria Dorigatti, Han Fu, Katy Gaythorpe, Will Green, Arran Hamlet, Wes Hinsley, Lucy C Okell, Sabine van Elsland, Hayley Thompson, Robert Verity, Erik Volz, Haowei Wang, Yuanrong Wang, Patrick GT Walker, Peter Winskill, Charles Whittaker, Christl A Donnelly, Steven Riley, Azra C Ghani.

On behalf of the Imperial College COVID-19 Response Team
WHO Collaborating Centre for Infectious Disease Modelling MRC Centre for Global Infectious Disease Analysis Abdul Latif Jameel Institute for Disease and Emergency Analytics Imperial College London
Correspondence: neil.ferguson@imperial.ac.uk

Summary
The global impact of COVID-19 has been profound, and the public health threat it represents is the most serious seen in a respiratory virus since the 1918 H1N1 influenza pandemic. Here we present the results of epidemiological modelling which has informed policymaking in the UK and other countries in recent weeks. In the absence of a COVID-19 vaccine, we assess the potential role of a number of public health measures – so-called non-pharmaceutical interventions (NPIs) – aimed at reducing contact rates in the population and thereby reducing transmission of the virus. In the results presented here, we apply a previously published microsimulation model to two countries: the UK (Great Britain specifically) and the US. We conclude that the effectiveness of any one intervention in isolation is likely to be limited, requiring multiple interventions to be combined to have a substantial impact on transmission.
Two fundamental strategies are possible: (a) mitigation, which focuses on slowing but not necessarily stopping epidemic spread – reducing peak healthcare demand while protecting those most at risk of severe disease from infection, and (b) suppression, which aims to reverse epidemic growth, reducing case numbers to low levels and maintaining that situation indefinitely. Each policy has major challenges. We find that that optimal mitigation policies (combining home isolation of suspect cases, home quarantine of those living in the same household as suspect cases, and social distancing of the elderly and others at most risk of severe disease) might reduce peak healthcare demand by 2/3 and deaths by half. However, the resulting mitigated epidemic would still likely result in hundreds of thousands of deaths and health systems (most notably intensive care units) being overwhelmed many times over. For countries able to achieve it, this leaves suppression as the preferred policy option.
We show that in the UK and US context, suppression will minimally require a combination of social distancing of the entire population, home isolation of cases and household quarantine of their family members. This may need to be supplemented by school and university closures, though it should be recognised that such closures may have negative impacts on health systems due to increased
16 March 2020 Imperial College COVID-19 Response Team
absenteeism. The major challenge of suppression is that this type of intensive intervention package – or something equivalently effective at reducing transmission – will need to be maintained until a vaccine becomes available (potentially 18 months or more) – given that we predict that transmission will quickly rebound if interventions are relaxed. We show that intermittent social distancing – triggered by trends in disease surveillance – may allow interventions to be relaxed temporarily in relative short time windows, but measures will need to be reintroduced if or when case numbers rebound. Last, while experience in China and now South Korea show that suppression is possible in the short term, it remains to be seen whether it is possible long-term, and whether the social and economic costs of the interventions adopted thus far can be reduced.
16 March 2020 Imperial College COVID-19 Response Team

Introduction
The COVID-19 pandemic is now a major global health threat. As of 16th March 2020, there have been 164,837 cases and 6,470 deaths confirmed worldwide. Global spread has been rapid, with 146 countries now having reported at least one case.
The last time the world responded to a global emerging disease epidemic of the scale of the current COVID-19 pandemic with no access to vaccines was the 1918-19 H1N1 influenza pandemic. In that pandemic, some communities, notably in the United States (US), responded with a variety of non-pharmaceutical interventions (NPIs) - measures intended to reduce transmission by reducing contact rates in the general population1. Examples of the measures adopted during this time included closing schools, churches, bars and other social venues. Cities in which these interventions were implemented early in the epidemic were successful at reducing case numbers while the interventions remained in place and experienced lower mortality overall1. However, transmission rebounded once controls were lifted.
Whilst our understanding of infectious diseases and their prevention is now very different compared to in 1918, most of the countries across the world face the same challenge today with COVID-19, a virus with comparable lethality to H1N1 influenza in 1918. Two fundamental strategies are possible2:
(a) Suppression. Here the aim is to reduce the reproduction number (the average number of secondary cases each case generates), R, to below 1 and hence to reduce case numbers to low levels or (as for SARS or Ebola) eliminate human-to-human transmission. The main challenge of this approach is that NPIs (and drugs, if available) need to be maintained – at least intermittently - for as long as the virus is circulating in the human population, or until a vaccine becomes available. In the case of COVID-19, it will be at least a 12-18 months before a vaccine is available3. Furthermore, there is no guarantee that initial vaccines will have high efficacy.
(b) Mitigation. Here the aim is to use NPIs (and vaccines or drugs, if available) not to interrupt transmission completely, but to reduce the health impact of an epidemic, akin to the strategy adopted by some US cities in 1918, and by the world more generally in the 1957, 1968 and 2009 influenza pandemics. In the 2009 pandemic, for instance, early supplies of vaccine were targeted at individuals with pre-existing medical conditions which put them at risk of more severe disease4. In this scenario, population immunity builds up through the epidemic, leading to an eventual rapid decline in case numbers and transmission dropping to low levels.
The strategies differ in whether they aim to reduce the reproduction number, R, to below 1 (suppression) – and thus cause case numbers to decline – or to merely slow spread by reducing R, but not to below 1.
In this report, we consider the feasibility and implications of both strategies for COVID-19, looking at a range of NPI measures. It is important to note at the outset that given SARS-CoV-2 is a newly emergent virus, much remains to be understood about its transmission. In addition, the impact of many of the NPIs detailed here depends critically on how people respond to their introduction, which is highly likely to vary between countries and even communities. Last, it is highly likely that there would be significant spontaneous changes in population behaviour even in the absence of government-mandated interventions.
16 March 2020 Imperial College COVID-19 Response Team

The Corona virus progression curve

This is one of the most important chart to consider in order to understand how different countries will fare against the Corona virus. From this, it is very clear that Asian countries are doing relatively well fighting the virus, European ones not so much. This will have consequences and may end up speeding up Asia's rise and conversely Europe's decline.

Understanding this trend from the Chinese data early on would have been extremely useful for the rest of the world. We lost about a month. From this data, a month is about two factors, so we can now expect that the Corona pandemic will be about 100 times larger than it should have been! 

Data mamagement progress

The data learning curve is steep.

To transform data into information, you need to format, clean, parse and segment the data.

To build knowledge, you must undestand the relations beetween data and create a system.

Insight is gained through experimentation and experience.

As for wisdom, I am not quite sure that "data" is the right starting point! 

The magic of haptic technology (video)

The progress of haptic technology are stunning! They offer the possibility to control complex layers of information in a easy and intuitive way, provided we work out intelligent interface. This is the next stage of technology where a whole virtual world will be created offering natural interaction and optimal control. But to really take off, this "world" need to be more secure than the current IoT, therefore probably based on blockchain technology, both distributed and decentralized, the opposite of the current trend. Privacy and people need to be placed back at the center of technological development. The alternative is a smart city for robots controlled by computers with no room left for humans. 

Creating a data catalog and understanding the importance of metadata

Creating a data catalog may indeed be the easiest way to understand and access data in a company. A data catalog is not about the data itself but about organizing meta-data. It is this organization which will eventually constitute the backbone of the database structure and efficient organization. Well worth a read, it only to understand better what is possible! #Data #Database #SQL #CRM #Datalake #Datawarehouse

https://www.datasciencecentral.com/profiles/blogs/a-step-by-step-guide-to-build-a-data-catalog

Introduction to anomaly detection (algorithm)

A rather interesting introduction to anomaly detection. Clear and instructive. This can have many applications beyond "vision" as the principle can be applied to all kind of data. #data #ML #database #machinelearning #machinelearningalgorithms
https://www.pyimagesearch.com/2020/01/20/intro-to-anomaly-detection-with-opencv-computer-vision-and-scikit-learn/

700 years of interest rates!

A surprisingly clear and impressive long term interest rates chart.

But what comes after "zero" when money is essentially free?Since we have just reached this point, we shall know very soon.

Is the Wuhan Corona Virus a bio weapon?

So is the Wuhan Corona Virus a bio weapon?

As reported earlier, the feedback we are receiving from China is very murky and difficult to interpret.

What we know so far is that the Wuhan virus also called nCoV, it's scientific name, is very contagious although it's real R0 (R naugh) is still difficult to calculate. Most estimates currently are between 3 and 4 which would be relatively high compared to other virus. (see below)

In reality, these numbers are statistical numbers with little actual meaning related to the future since they can vary wildly over time. A contagion may start with a high R0 to see this number later dwindle as measures are taken to isolate sick persons and contain the outbreak. More important to the global spread of the virus is how it propagates between people. A long lasting virus like HIV which propagates through sexual transmission will see a slow be steady propagation ending up with a relatively high R0 whereas the flu with a lower R0 will spread much faster through the air in spite of its low rate of transmission. The worst virus known is the measles virus with a maximum R0 of 18 which can linger in the air for over 2 hours. In between, you find Zika which transmits through mosquitoes and nCoV which transmits through the air like the flu.

The second important factor is the death rate. As of today, Tuesday, February 4th the death toll is 425 but this number is highly unreliable. Although the Chinese authorities have done some efforts to become more transparent lately, initially the dead were not reported and it is still likely that many deaths are voluntarily or not misdiagnosed as other causes such as pneumonia. (In many cases it may just be because there is no diagnostic kit available!)

If we compare the fatality rate of the Corona virus to other virus, it looks relatively low at about 2%. It is still low if you double this number which may be a good estimate. (But in that case, we can also double the number of cases and end up with a similar 2% fatality rate.)
 
This has been used as an argument against the virus being a bio weapon since such a weapon would by definition have a high fatality rate. But in reality, the fatality rate is just one factor among many. Another is the number of serious cases necessitating intensive care which at over 25% is very high.

The most damning accusation to date that the virus may be a weapon came from a team based in India which asserted that studying the genome of the virus they found 4 insertions which had similarities to the genome of HIV. In this respect, it is important to note that the research was not peer reviewed and has since been retracted. Other scientists have noted that these codons are not specific to HIV and can be found in many virus including other Corona Virus so not a proof as such.

This said, it is widely reported that patients with Corona Virus respond well to HIV treatments... Again, not conclusive but certainly an interesting factor to take into consideration.

More interestingly, running the Blast statistical software on the genome of nCoV shows that 89% of this genome comes from the NG strand of SARS with some nucleotides from the KY strand which code the S-protein. The S-protein being the part of the genome which codes what binds the virus to human tissues in the lung. Reason why is appears as pneumonia and pass on so easily from people to people.
(source)
 
All this remains to be proven.

In the scientific literature, it is obvious that conclusions are closely linked to the genetic models as well as the assumptions you are using and that no consensus has yet been found on the origin of the virus beyond the fact that it is originally, probably, a bat virus which has mutated significantly.

So the original question can now be rephrased:

Knowing that the outbreak happened in Wuhan, the only city with a P4 level laboratory in China, that the virus has characteristics from different strands of the Corona Virus which makes it especially virulent and contagious, and that the virus seems to be able to propagate during the incubation phase when people show no signs of being sick, a relatively rare characteristics, could this virus be a bio weapon?

Virus do evolve naturally. This is why, more or less every year we have a new strand of the flu. They are also known in some instance to exchange part of their genome with other virus.  To answer more precisely the question, we now need to understand better the genome of nCoV. (The fact that the genome has been decoded does not mean that we understand the details of its origin and evolution yet.)

Many teams around the world are working on this subject so the answer should be clear within a month.

Still, although the damning evidences may be circumstantial, it is clear that China has spent a month from mid December to mid January trying to silence doctors who were warning us about the outbreak. Then when the scale of the pandemic became clear, the country took extreme measures by isolating a whole city, then a whole province while reassuring people that everything was under control and not as bad as anecdotal reporting suggested. Sure enough, it was worse!

The suppression of information and obfuscation is in the DNA of the Chinese government. This alone does not prove fool-play. Still altogether, all these factors are difficult to explain as pure coincidence. Statistics allow unlikely events to occur but beyond a threshold that the Corona Virus seems suspiciously close to, a human helping hand becomes the simpler explanation. So although it cannot be said yet that the nCoV virus is a bio weapon, the assertion cannot be dismissed out of hand so easily either. The possibility that Chinese scientists where indeed working on dangerous pathogens with the aim to eventually transform them into weapon as some like Dr Francis Boyle have accused them of doing although difficult to prove is real.   

The end is near / (Programmer's joke!)