Saturday 28 March 2020

The Mistakes on Relying on Case Fatalities

https://www.npr.org/sections/goatsandsoda/2020/03/27/821958435/why-death-rates-from-coronavirus-can-be-deceiving

The faster you test the lower the case fatalities will surely be because those tested will not die immediately.

"In Italy, about 10% of people known to be infected have died. In Iran and Spain, the case fatality rate is higher than 7%. But in South Korea and the U.S. it's less than 1.5%. And in Germany, the figure is close to 0.5%."

These figures are low because many of these haven't died yet. Wait for a few more days, then many will die eventually.

This common sense does not seem to be obvious to these idiots.

The best data is the number of closed cases. Once a person is tested positive, he is monitored either in hospital or at home, depending on the severity of symptoms and availability of hospital beds. If they can be discharged, his case is closed, i.e. he recovered or vice versa. So, closed cases are the real measure of fatality, certainly not case fatalities.

The lowest figure, based on John Hopkins data, is China, at 4%.

 U.S.A. is still too early to tell but Italy is 45%. Spain 32%
https://www.worldometers.info/coronavirus/country/italy/ today, 28 March, 2020.
What it shows is that Italy's hospitals are overwhelmed. Spain is under severe strain.


Why 'Death Rates' From Coronavirus Can Be Deceiving

Coffins of deceased people stored in a warehouse near Bergamo — a city at the heart of Italy's coronavirus crisis — before being transported to another region for cremation.
Piero Cruciatti/AFP via Getty Images
The coronavirus appears to be much more lethal in some countries than in others.
In Italy, about 10% of people known to be infected have died. In Iran and Spain, the case fatality rate is higher than 7%. But in South Korea and the U.S. it's less than 1.5%. And in Germany, the figure is close to 0.5%.
So what gives?
The answer involves how many people are tested, the age of an infected population and factors such as whether the health care system is overwhelmed, scientists say.
"Case fatality rates have been very confusing," says Dr. Steven Lawrence, an infectious disease expert and associate professor of medicine at Washington University School of Medicine in St. Louis. "The numbers may look different even if the actual situation is the same."
So it's likely that the seemingly stark difference between Germany and Italy is misleading and will diminish as scientists get more data, Lawrence says.
Also, because of the way countries monitor pandemics like the coronavirus, he says, the case fatality rate tends to decrease over time. The reason: When a new disease first shows up, testing usually focuses on severely ill people who are at high risk of dying. Later on, testing is more likely to include people with milder illness who are less likely to die.
That's what happened with West Nile virus, which appeared in the U.S. in 1999. At first, when scientists only knew of about a few dozen cases, it appeared the mortality rate was higher than 10%. But wider testing eventually found hundreds of thousands of people who'd been infected but never got sick enough to notice. Today, more than 3 million Americans have been infected and studies show that fewer than 1% become seriously ill.
If that pattern holds for coronavirus, countries such as Italy, which have been testing only the sickest patients, are likely to see their case fatality rates fall. But countries such as Germany, which has been testing both critically ill people and those with milder symptoms from the beginning, are less likely to see major changes in the case fatality rate.
The U.S. is somewhere in between. Testing was severely limited when cases started to appear. Since then labs have begun testing tens of thousands of people with less severe illness.
A country's case fatality rate is simply the number of deaths (the numerator) divided by the number of infections (the denominator). The problem is, both of these numbers may be unreliable.
For example, when an outbreak begins and health officials aren't looking for the virus, some people may die at home and never be diagnosed. That would lower the numerator and "might lead to an underestimate of the case fatality rate," Lawrence says.
But a much more likely scenario, he says, is that early in an outbreak, testing is limited to people who are so sick they wind up in the hospital. That means the only infections that get counted are in the people most likely to die. So the denominator is missing a huge number of infected people who survive, and that makes the virus appear much more deadly than it really is.
This is probably one reason that early death rates in China appeared so high, says Gerardo Chowell, a professor of epidemiology and biostatistics in the department of population health sciences at Georgia State University. Chowell is part of a team that has been using statistical modeling to study the outbreak in China and South Korea.
When cases started showing up in the city of Wuhan, Chinese health officials "were obviously caught by surprise" and lacked the ability to test many patients, Chowell says. So testing was restricted to the sickest people. That probably contributed to early evidence that the fatality rate in Wuhan was 4% or more.
A study published last week estimated that in Wuhan, the chance that someone who developed coronavirus symptoms would die was actually 1.4%.
In South Korea, though, "they have been doing massive testing" since the first cases were detected, Chowell says. As a result, that nation has been able to count infected people with mild symptoms as well as those who become severely ill. That may be one reason the case fatality rate in South Korea has remained below 2%.
Another factor affecting coronavirus fatality rates is the characteristics of the population that is infected at any given moment, says Mary Bushman, a postdoctoral researcher at Harvard's Center for Communicable Disease Dynamics and an author of the Wuhan study.
In Washington state, Bushman says, the first cases appeared in nursing home residents, who tend to be extremely vulnerable to the disease. That produced "an alarming number of deaths being reported," Bushman says. At one nursing home, 34 of 81 infected residents died, which is a case fatality rate of 42%.
But as Washington began testing for the virus outside the nursing home, it became clear the case fatality rate in the general population was vastly lower.
And across the U.S., as testing has expanded to include younger and healthier segments of the population, the fatality rate has decreased to levels similar to those in South Korea. "And I think we'll probably continue to see further decreases," Bushman says.
Differences in testing aren't the only reason that case fatality rates vary, though. In some countries, infected people have been more likely to die because the health care system has been overwhelmed, leaving critically ill coronavirus patients without access to lifesaving care, Chowell says.
In Wuhan, he says, high case fatality rates early on were probably caused in part by the inability of local hospitals to handle the huge influx of patients sick with the coronavirus.
An overburdened health care system may also be contributing to the high case fatality rate in Italy. "During those high peaks where the health care systems can be overwhelmed, there may not be enough people or ICU beds or ventilators to be able to provide the critical care that is needed," Lawrence says.
Ultimately, it will take a different sort of test to assess how lethal coronavirus has been, Lawrence says. Most current tests only detect active infections — when the virus is still present in the body. But a different type of test — now being developed but still probably months away from wide use — can reveal whether a person has ever been infected. And that is what scientists need to know to establish the true denominator for coronavirus and to find the true case fatality rate.
In the U.S., it's likely that the case fatality rate from coronavirus will end up somewhere between 0.5% and 1%, once a broad cross-section of the population has been tested, Lawrence says.
But that's no reason for the nation to relax, he adds.
"To put it into perspective, that's 5 to 10 times more fatal than flu," Lawrence says, a disease that kills between 12,000 and 61,000 people a year.

Stupid Imperial College Estimate

https://www.imperial.ac.uk/news/196496/coronavirus-pandemic-could-have-caused-40/

Imperial College is among the highest ranked universities in the world, alongside MIT. Usually among the top is MIT but surprisingly MIT researchers are silent on Covid-19, not even daring to provide an estimate.

These rankings are based on citations i.e. researchers quoting each other's work. As can be expected, they led to in-breeding. They cannot even see obvious errors let alone the needs of the world.

"According to the unmitigated scenario, if left unchecked the virus could have infected 7 billion people and caused in the region of 40 million deaths this year."

Completely wrong data

Where does they get this data? 40 million out of 7 billion is 0.57%
This is a case fatality rate in the early days, which should never be used in calculating fatality rates because it grossly underestimate fatalities for fast rising cases. This should be obvious for those who understand maths and had been pointed out by MIT during the SARS pandemic and recently by an expert in Hong Kong.

https://www.nytimes.com/2020/02/10/opinion/coronavirus-china-research.html
SARS was initially estimated to be 2% to 3% but was actually 17%, taking into account the treatment time.

https://www.worldometers.info/coronavirus/country/china/
The fatality rate for closed cases is 4%, with 96% recovered.
This is a more reliable figure.

https://www.worldometers.info/coronavirus/country/italy/
For Italy it is 45% but this is an example of overwhelmed hospitals.
But its case fatality rate which was used by the study by Imperial College is 9,134 deaths divided by the number of cases, 66,414, so it is just 14%.

Which figure should be use to estimate fatality, which is just the probability that you will die? Should you divide the number of deaths with the number of new cases, or should it be divided by the number of closed cases, i.e. the number of recovered cases plus deaths. Those cases will take time to die, 14 more days so they appear to lower the percentage of deaths.

 https://www.forbes.com/sites/victoriaforster/2020/03/22/what-have-scientists-learned-from-using-cruise-ship-data-to-learn-about-covid-19/#52019e22406d
"712 people infected on board, eight so far are known to have died"

https://www.livescience.com/new-coronavirus-compare-with-flu.html
"44,672 confirmed cases in China between Dec. 31, 2019 and Feb. 11, 2020. Of those cases, 80.9% (or 36,160 cases) were considered mild, 13.8% (6,168 cases) severe and 4.7% (2,087) critical. "Critical cases were those that exhibited respiratory failure, septic shock, and/or multiple organ dysfunction/failure," the researchers wrote in the paper published in China CDC Weekly."

The danger is the 19% that are severe cases that will die if not hospitalised.

Completely wrong assumption


My main idea of writing this article is just to point the most important stupidity. The stupid assumption that hospitals will never be overwhelmed.

Even if we were to take the figure of 0.57% figure, this figure assumes that all patients can be treated in hospitals. Once they are not treated, they will surely die.

Therefore the correct figure should be 19%, which is  1,260 million, if no social distancing or isolation is carried out. Certainly not 40 million.

Deaths if all infected

If all 7,000 million people were infected, then the fatality rate of 4% should be used, certainly not the case fatality rate of 0.57%. Which means that 280 million will die, even if we assume that all can be treated at hospitals.
So the correct figure should be between 280 million to 1,260 million will die in this pandemic if everyone on earth were to be infected.


Real solutions

The only hope is to stop it from infecting people before a vaccine can be produced. This can only be achieved by strict quarantine and isolation procedures that assume that everyone is infected.

We can avoid quarantine if we can test every single person who wants to travel instead of quarantining them but even these tests must be done at 3-day intervals for at least 3 times. This assumes that the mean incubation period is 3 days.



Coronavirus pandemic could have caused 40 million deaths if left unchecked

by

Concept of the planet surrounded by viruses

The outbreak of COVID-19 would likely have caused 40 million deaths this year in the absence of any preventative measures.
This is one of the findings of a new analysis by researchers at Imperial College London, which estimated the potential scale of the coronavirus pandemic across the globe, highlighting that failure to mitigate the impact could lead to huge loss of life.
The report is the twelfth to be released by The WHO Collaborating Centre for Infectious Disease Modelling within the MRC Centre for Global Infectious Disease Analysis (GIDA), Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA).
Researchers included a number of scenarios, such as what would have happened if the world had not reacted to COVID-19 (the “unmitigated scenario”). They also included two scenarios incorporating social distancing, which result in a single-peaked epidemic (“mitigated scenarios”), and several scenarios for suppressing the spread of the disease that can have the largest overall impact in terms of reducing disease and deaths.
Rapid, decisive and collective action is required by all countries to limit the effect of this pandemic Prof. Azra Ghani MRC GIDA
According to the unmitigated scenario, if left unchecked the virus could have infected 7 billion people and caused in the region of 40 million deaths this year. Social distancing to reduce the rate of social contacts by 40 per cent, coupled with a 60 per cent reduction in social contacts among the elderly population (at highest risk) could reduce this burden by around half. However, even at this level of reduction, health systems in all countries would be rapidly overwhelmed, the modelling revealed.
Dr Patrick Walker, an author of the report from Imperial, said: "We estimate that the world faces an unprecedented acute public health emergency in the coming weeks and months. Our findings suggest that all countries face a choice between intensive and costly measures to suppress transmission or risk health systems becoming rapidly overwhelmed. However, our results highlight that rapid, decisive and collective action now will save millions of lives in the next year"

Proven health measures

In the latest report, the team show that rapid adoption of proven public health measures – including testing and isolation of cases and wider social distancing to prevent onward transmission – are critical in curbing the impact of the pandemic.
Professor Azra GhaniThe modelling showed that implementing measures early on can have a dramatic impact.
If all countries were to adopt this strategy at 0.2 deaths per 100,000 population per week, 95 per cent of the deaths could be averted, saving 38.7 million lives.
However, if this strategy is adopted later (1.6 deaths per 100,000 population per week), then this figure drops to 30.7 million.
“Rapid, decisive and collective action is required by all countries to limit the effect of this pandemic,” said Professor Azra Ghani, report author from MRC GIDA.
“Acting early has the potential to reduce mortality by as much as 95 per cent, saving 38.7 million lives. At the same time, consideration needs to be given to the broader impact of all measures that are put in place to ensure that those that are most vulnerable are protected from the wider health, social and economic impacts of such action.”


Penalty for ignoring Evidences in Wuhan Virus

https://www.bbc.com/news/world-us-canada-52056586

This is the result of the evidence-based decisions. Or rather no-evidence decisions.

So much evidences from China had been ignored and censored with idiotic and arrogant explanations. Worse, the world is silent even in the face of these idiocies.

What has happened to all the intelligent people that are supposed to publish and disseminate knowledge to the masses?

Why is that it is only now that people realise that they need ventilators now? Has the world become so stupid?

Wasn't it obvious given the large amount of knowledge that were published and as recently provided by China, Hong Kong and South Korea? Why are they all ignored or rather censored?

I don't think Covid-19 is as infectious as Ebola or SARS. They are just about the same infectiousness. The only difference is that symptoms are not obvious and cannot be detected but it was reported in China months before, but how many doctors believe in this? Virtually none. Even now.

Look at the WHO, USA, Malaysia and Singapore policies. They still test body temperatures and not insisting on ANY QUARANTINE AT ALL. Even now. Really reckless and stupid and certainly not based on any evidence at all.

Worst, they still insist on doing lockdowns that are leaky and costly. Just implement quarantines at all borders and enforce them the cheapest way possible. This is standard procedure in any infectious disease control.

Even Sabah, that has the opportunity to close its borders, had not done so. Similarly for Sarawak. Closing borders with Singapore but not Italy. Why not the whole world? Even against West Malaysia.

Are doctors so stupid that they think they can implement leaky quarantines? Is there any intelligent doctor left given the silence from any of them on the reckless and stupid decisions that had been implemented.

Of course, the victims will be the doctors themselves.

For Muslims have to pay the price for breaking the laws of Islam.

Dayus, i.e. silent when they see something wrong. This is the second most sinful action that a Muslim can commit, even worse than murder, which is this case in certainly correct.

Ignoring the lock-down rules in Islam despite it being clearly stated in the sayings of the prophet.

Era of Online Lectures and Tutorials

I have decided to implement online lectures and tutorials for all my courses, using Google Meet and Smart Hadir.

Software Required

Microsoft Windows browser:
Google Meet

Android Apps:
Android Hangouts Meet

Apple iOS Apps:
iOS Hangouts Meet

Android Smart-Hadir

iOS Smart-Hadir

Procedure

This means that I do not require students to attend my lectures and tutorials any more.
Their attendances can be verified by using Smart-Hadir, chat and video recording of student.
I would require students to switch on their camera all the time but switch off their microphone unless they want to ask questions that cannot be written down in the chat.

All the sessions will be recorded for students to refer to and qualifying agencies to verify the standard of teaching and attendances.

UMS has a license to Google Meet but Hangouts Meet is supposed to be limited to 30 users. I managed to get 31 students out of 45 in total.

Hangouts Meet Specifications

Extracted from Hangouts Meet apps description:
Key features include:
• High-definition video and audio meetings with up to 250* participants






Not sure how high but students can read large texts but not small texts in my FULL HD, 1920 x 1080 screen, and I have no way of controlling the resolution of the presentation, i.e. the video that is sent to the users. I can only control the video of presenter and receiver from 720p to 360p but the image quality actually isn't obvious between them.

You can present just a window or the entire screen. I thought full screen presentation will slow it down so much that the voice is distorted. It does not appear to be so, if we disable the video camera from the students.
 
• Real-time captions powered by Google speech-to-text technology

I used it by enabling the caption. Useful in order to check the quality of my spoken English.

• Easy access - just share a link and anyone can join with one click from desktop or mobile

This is verified. They can use any email and their names are actually recorded in the chat. These are probably extracted from the Android and Apple accounts in their phones.

Possible Problems

It is possible that the cost of data is too high for students but travelling cost is even higher. Not to mention other costs. The possibility of low bandwidth areas even in Sabah is very low. If signal is too low, they can move to a different place where signal is good. Even on top of a hill if required.

Saturday 14 March 2020

Maths of Sporadic Infections

A staff at Sultan Salahuddin Abdul Aziz Shah mosque in Shah Alam, squeezes out hand sanitiser on to a palm of a person, amid the Covid-19 coronavirus outbreak. - BERNAMA pic
KUALA LUMPUR: Medical experts are urging for faster and urgent action in handling the Covid-19 outbreak in the country.
This follows the World Health Organisation’s declaration of the disease as a pandemic on Wednesday, and the tabligh gathering at the Seri Petaling Mosque here recently, which sparked a new cluster transmission of Covid-19 in the country.
Dr Ong Hean Teik, past chairman of the Penang branch of the Malaysian Medical Association, said the situation in Malaysia was severe and this warranted stricter measures.
This, he said, included banning mass gatherings, postponing weddings and events, as well as closing down schools temporarily in high-risk areas.
“The virus is present in the community. We not only have cluster cases (sparked by Cases 26 and 131), but we have also entered the community transmission stage, which calls for the authorities to boost its emergency response mechanism.
“Issuing an advisory is not enough. The Health Ministry should be clear in conveying the seriousness of the outbreak.
“Malaysia was successful in containing the spread during the first wave. Case 26 changed this. Since Cases 26 and 131 contracted the virus in Malaysia, isn’t it enough to indicate community spread?
“People need to be informed to contain the virus.”
Dr Ong, a consultant cardiologist and past president of Penang Medical Practitioners’ Society, said medical practitioners, including head of departments at public hospitals, had raised concern about the shortage of Covid-19 test kits.
This, he said, was causing a backlog in case detection, especially following the tabligh gathering where thousands of people were scrambling to get tested.
He questioned if the ministry had adequate resources in place if the outbreak worsened.
People wearing face masks at Kuala Lumpur International Airport in Sepang yesterday. -BERNAMA pic
“WHO’s data suggests that 80 per cent of Covid-19 infections are mild or asymptomatic, 15 per cent are severe infections requiring oxygen and five per cent are critical infections requiring ventilation.
“How many ventilators and extracorporeal membrane oxygenation machines do we have for those with respiratory failures? Do we have sufficient protective gear for medical personnel?”
Former Malaysian Medical Association president Datuk Dr N.K.S. Tharmaseelan agreed that Malaysia had entered the community transmission stage. He advised the public to take extra precautions.
Malaysian Public Health Medicine Specialist Association president Datuk Dr Zainal Ariffin Omar said the Health Ministry should make public the list of places that Covid-19 patients had visited, worked at or areas they lived in.
This, he said, was so that the public could practise social distancing.
Paediatrician Datuk Dr Musa Mohd Nordin said the asymptomatic transmission of Covid-19 made total containment difficult and problematic.
He said there might be a need to realign and reconsider some of the Health Ministry’s strategies of containment and mitigation.
“I do not think we need to follow the lockdown methodology of China and Italy. South Korea has been successful in reducing the number of confirmed cases of Covid-19 from 900 per day to fewer than 100 per day.
“We can learn from South Korea’s strategy. We must ensure that there are sufficient diagnostic test kits.
“South Korea undertakes 12,000 to 20,000 tests per day.
“To facilitate testing, South Korea has set up drive-through Covid-19 test centres. This drive-through model has been replicated by KPJ Damansara Specialist Hospital (KPJ-DSH) and Sungai Buloh Hospital.
“KPJ-DSH has operated drive-through test centres at the premises of government-linked companies to test those who had close contact with Case 26.”
Dr Musa said it was crucial to be transparent in information sharing because access to accurate information could debunk fake news and fearmongering.
“It empowers the people to be active partners of the Health Ministry and the government in the fight against the outbreak.”