Update on Coronavirus

 

Saturday, April 18, 2020

Update on Coronavirus

Reproduction

Update on Coronavirus

This retrospective case series includes adults 18 years of age or older with confirmed Covid-19 who were consecutively admitted between March 5 (date of the first positive case) and March 27, 2020, at an 862-bed quaternary referral center and an affiliated 180-bed nonteaching community hospital in Manhattan. Both hospitals adopted an early-intubation strategy with limited use of high-flow nasal cannulae during this period. Cases were confirmed through reverse-transcriptase–polymerase-chain-reaction assays performed on nasopharyngeal swab specimens. Data were manually abstracted from electronic health records with the use of a quality-controlled protocol and structured abstraction tool (details are provided in the Methods section in the Supplementary Appendix, available with the full text of this letter at NEJM.org).

Table 1. 

Characteristics of the Patients.

Among the 393 patients, the median age was 62.2 years, 60.6% were male, and 35.8% had obesity (Table 1). The most common presenting symptoms were cough (79.4%), fever (77.1%), dyspnea (56.5%), myalgias (23.8%), diarrhea (23.7%), and nausea and vomiting (19.1%) (Table S1 in the Supplementary Appendix). Most of the patients (90.0%) had lymphopenia, 27% had thrombocytopenia, and many had elevated liver-function values and inflammatory markers. Between March 5 and April 10, respiratory failure leading to invasive mechanical ventilation developed in 130 patients (33.1%); to date, only 43 of these patients (33.1%) have been extubated. In total, 40 of the patients (10.2%) have died, and 260 (66.2%) have been discharged from the hospital; outcome data are incomplete for the remaining 93 patients (23.7%).

Patients who received invasive mechanical ventilation were more likely to be male, to have obesity, and to have elevated liver-function values and inflammatory markers (ferritin, d-dimer, C-reactive protein, and procalcitonin) than were patients who did not receive invasive mechanical ventilation. Of the patients who received invasive mechanical ventilation, 40 (30.8%) did not need supplemental oxygen during the first 3 hours after presenting to the emergency department. Patients who received invasive mechanical ventilation were more likely to need vasopressor support (95.4% vs. 1.5%) and to have other complications, including atrial arrhythmias (17.7% vs. 1.9%) and new renal replacement therapy (13.3% vs. 0.4%).

Among these 393 patients with Covid-19 who were hospitalized in two New York City hospitals, the manifestations of the disease at presentation were generally similar to those in a large case series from China¹; however, gastrointestinal symptoms appeared to be more common than in China (where these symptoms occurred in 4 to 5% of patients). This difference could reflect geographic variation or differential reporting. Obesity was common and may be a risk factor for respiratory failure leading to invasive mechanical ventilation.³ The percentage of patients in our case series who received invasive mechanical ventilation was more than 10 times as high as that in China; potential contributors include the more severe disease in our cohort (since testing and hospitalization in the United States is largely limited to patients with more severe disease) and the early-intubation strategy used in our hospitals. Regardless, the high demand for invasive mechanical ventilation has the potential to overwhelm hospital resources. Deterioration occurred in many patients whose condition had previously been stable; almost a third of patients who received invasive mechanical ventilation did not need supplemental oxygen at presentation. The observations that the patients who received invasive mechanical ventilation almost universally received vasopressor support and that many also received new renal replacement therapy suggest that there is also a need to strengthen stockpiles and supply chains for these resources.

Parag Goyal, M.D.
Justin J. Choi, M.D.

Coronavirus-01

 

Sunday, April 12, 2020

COVID-19: Ceylonese Response

My Comments

I have made adequate entries on this virus (not the epidemic) at this site!

Our failure to "nip in the bud" were obvious even though government doctors (not GMOA, who bum-sucks politicians) did a creditable job.

We were lucky that we were not a tourist destination for many except Chinese and Indians (that is also for commercial exploitation) after Church Bomb and Wahabis activities which Sirisena ans Ranil failed to address. That included Mahinda too, he did not suppress its activities emerging way back in 2008 fearing loss of Muslim vote.

Cash struck we relied on Chinese and allowed a Visa Office for Chinese to operate without supervision.

Very stupid political action.

I have a saying, "Never trust a Chinaman" that includes SOHO in London.

The only difference between Indians (RAW and Gandhi's) and Chinese is very simple.

Indians get caught lying but Chinese never get caught with the HELP of WHO with an Ethiopian heading it shamefully.

When India and Africa get affected there is no stop of it spreading like a wildfire (poor sanitation, lack of water, malnutrition, poverty and joblessness compounding).

We may have to go back to hand to mouth existence (with unbearable debts and nobody giving a free lunch- an euphemism of mine) and NM and Sirima Era of Pan Poling-Bread queues and Manioc and Batala.

History repeats itself and SLFP/SLPP (I call it Pathala Party) unlike the UNP cannot feed the masses, especially in the North!

It is like Un SuKi of Myanmar taming the Army.

Very soon we won't be able to tame the emerging army influence on politics.

Thankfully our Police Force kept them at bay! 

Above are SAD realities (only a few mentioned).

COVID-19: Ceylonese Response

Emerging Questions, Testing Times

Reproduction

Rajan Philips

It is now one month after the WHO declared Covid-19 a global pandemic. Some clarity is emerging through the viral cloud about what happened, what went wrong and what might have been done differently. It is legitimate to ask if Wuhan had to be isolated from the rest of China, why could not China have been isolated from the rest of the world. Had that twin isolation been undertaken, China would have got reconnected with the world in 67 days at most, the time it took China to end the isolation of Wuhan. In fact, China’s external isolation would have ended a lot sooner. Trade connections and supply chains would have survived an immediate isolation with minimum disruptions, and would not have been catastrophically broken as they are now. 

This is all now hindsight, but the questions to China and the WHO are not going to go away.

There is plenty of blame to go around the world for general government inertia as well as sinister political calculations. Early warnings were ignored in the US and pandemic emergency plans meticulously prepared in western countries after the SARS crisis were not even looked at this time. 
The exceptions are the few East Asian countries, perhaps Australia and New Zealand down under, and Iceland and Denmark up north. There are broader questions as well – from the direct connections between the growth of global agri-business and the release of pathogens from their harmless natural settings to hit and harm human hosts, and the diminishing global investment in the study of and preparedness for communicable diseases relative to lifestyle illnesses. But the questions and the debates will have to wait for another day until the current fight against the virus is brought under control.

There is no primeval fight or flight option. But fight and feed. Fight the virus, feed the people. That is the task of every government and it cannot get more basic for any government. And the task should not be made more difficult by the all too familiar lapses into never ending spats over race, region and religion. When nothing works, blame the unreliable Chinese or the ugly American. If neither works, blame the Muslims, especially in South Asia. The European Union that was created to end its recurrent internal wars is warring again over supplies and subsidies in the fight against the virus. And for the great NATO, it is business as usual. They will get paid for doing nothing as usual, or for desk-top testing of non-existent pandemic scenarios, unlike everyone else in the world.       

Oh, yes, “April is the cruelest month.” T.S. Eliot would never have imagined that the famous opening line of his melancholy poem, The Waste Land, would turn out to be a morbid prophesy not only for the country of his birth, but also for the country of his adoption. The United State of America, where Eliot was born, is now the epicentre of a global pandemic. And the United Kingdom, of which he became a citizen after renouncing his American citizenship, is faring proportionately the same, if not worse. Prime Minister Boris Johnson himself has become a prime patient of Covid-19. Mr. Johnson is reportedly recovering well, after being in intensive care unit but without needing ventilator support, and much to the relief of a Brexit-battered and virus-hit nation. In general, however, and as usually alarmingly in the US, marginalized people are faring the worst.

The number of Covid-19 cases and deaths worldwide keep rising relentlessly. There are different lights in different tunnels. Europe seems to be on the mend finally, but only through a mountain of the dead. In the US the virus is surging in one state after another, but the curve appears to be flattening in general. Africa is no longer immune as it appeared to be at the start, and the worst is yet to come both for the continent’s health and its economy. East Asia is relatively stable, including China the origin of the viral quake. South Asia is sitting somewhat precariously in the middle, with India looming as the huge known unknown. That is the current picture and also the context for ongoing decision making.

Decision Making

Decisions are now being made in three interlocking planes, the science about the virus, the public action to contain its transmission, and governmental efforts to cushion the economic fallouts. The practical side of the science about the virus is all about testing. It is the paucity of testing and the lack of sufficient knowledge about the virus that has made contact tracing and physical distancing – from simple home isolation, to centralized quarantines, to total lockdowns - the only way to break the chain of transmission and stop the viral spread.

It is the same paucity that has given rise to two, rather crude but the only available, universal metrics in the tracking of the virus and the fighting of its transmission: the number of days it takes to double the number of Covid-19 cases; and the number of tests per million population. The former helps in plotting the curve and the latter to assess the extent of the virus spread and to see if and how containment measures are working. For comparison, in the pandemic hotspots like China, Italy, Spain and the US, the number of days during which cases doubled, shrank from six to seven days at the start to three to four days during the surge.

Sufficient testing is needed to decide how and when the current isolation and distancing could be relaxed, and in what stages. Until then, there are economic fallouts to be taken care of. Unlike any of the past economic upheavals, the current shutdown is the worst supply side crisis ever, and writ large over the world like never before. While during the 2008 Great Recession, the western countries were hit hard and the peripheral economies were relatively spared, it is the global periphery that will be hit harder than the economic centres in the current showdown. Global initiatives have been either promised or called for by G20 leaders ($5-trillion), the UN ($9-trillion) and a large group of former world leaders ($5-billion) – that includes President Chandrika Kumaratunga. If any or all of them were to materialize, that would ensure a significant cashflow to peripheral countries. But how soon and how much are indeterminate, and the current beggar-thy-neighbour attitude to one another among the  western countries does not augur well for much global certainty.    

Testing delays have been universal, except again for the few East Asian countries. Even the US got tied up in regulatory knots and wasted precious time in the beginning before ramping up its testing program. The countries that are doing better in containing the virus are also doing larger number of tests than others. South Korea and Singapore are at 9,000 and 12,000 tests per million people, respectively. Australia is at 13,000 tests per million people, while Bahrain and Iceland are off the charts at 35,000 and 89,000 (multiple) tests per million. Timing is important. Germany and Italy are doing 15,000 tests per million, but they started late, especially Italy. France and England are under 5,000 tests per million, while the US and Canada are hitting close to 7,000 and 10,000 tests, respectively, but with significant regional variations.

Testing time for Sri Lanka

By all accounts, Sri Lanka has done phenomenally well in contact tracing and supervised quarantining. The record on testing, however, is nowhere near as good. Currently, the tests are reportedly limited to patients only, and about 3500 tests have been carried out so far according to recent news reports. That would place Sri Lanka at about 175 tests per million people, and in the same South Asian camp as Bangladesh at 36 tests per million (with 6,000 tests), India at 107 (145,000 tests), and Pakistan at 212 (45,000 tests). Sri Lanka has been conducting 150 to 300 tests daily, although it is said to have the capacity to go up to 1500 tests a day. At this rate, it will take just over two months to reach a reasonable target of 5000 tests per million (i.e. 100,000 tests). There have also been suggestions that the daily test rate can go up to 12,000 tests a day, but there has been no follow up regarding an aggressive testing program  

There is then the debate, including in Sri Lanka, about what tests to perform and who should be targeted for tests. The primary test type is the diagnostic laboratory PCR (Polymerase Chain Reaction) test that detects the virus and confirms infection in a person. Multiple tests are needed in some cases before infection is confirmed. In many jurisdictions, this test and confirmation are required for ‘treating’ patients, even though, as some epidemiologists and physicians have pointed out, there is no accredited therapy for Covid-19.

The WHO definition of a confirmed case as “a person with laboratory confirmation of COVID-19 infection”, gives PCR test a special imprimatur. Dr. Jayaruwan Bandara, Director of the Medical Research Institute, has called it “the gold standard test” for diagnosing Covid-19. Understandably so, and the same token entails many restrictive guidelines for carrying out the test. The lab work invariably takes time and it has taken too much time even in western countries to increase the laboratory throughput of test results.

In addition, the PCR test is not a mass surveillance test to assess the spread of infection in a community. Hence the call for a second test, the serology test, that detects the antibodies that are produced to fight the virus infection. This can be used for both diagnosis and for population surveillance that will show the number of people who have been infected, including those with minor symptoms and those who are asymptomatic. Detecting asymptomatic cases is the special advantage of the serology test, knowing that asymptomatic transmission of the coronavirus is what renders it intractable.

As against these merits of serological testing, there is conventional reluctance in (government) medical and health regulatory circles to implement a serological testing program at the early stages of an epidemic. The reluctance might be because the regulatory agencies are not prepared to apply the serology test for diagnostic purposes insofar as the test does not detect the virus or early infection. Serology tests are typically used after an epidemic to assess the levels of infection and immunity in the community to prepare for the next outbreak. This point has also been made by the Director General of Health, Dr. Anil Jasinghe, who has indicated that “PCR is the test that was used by China and South Korea, at the initial stage of Covid-19, and that tests, like blood antibody testing, were used later.” The Sri Lanka Medical Association (SLMA) has also called for expanding PCR testing instead of shifting to serology testing.

On the other hand, the GMOA, in my understanding from news reports, has been pressing for implementing a rapid (serology) test program, and to carry out tests among 45,000 or so ‘contact traces’, who are in quarantine and are yet to be tested. In between, Chair Professors of Medicine (and specialist Physicians) from six of the island’s medical faculties, in their letter to Lt. Gen. Shavendra Silva, Chairman of the Covid-19 National Task Force and Dr Anil Jasinghe, Director General of Health Services, recommending next steps, have called for increasing test capacity and to “seek advice from virologists regarding what tests are most appropriate for use in specific scenarios.”

Across the world, a Canadian epidemiologist, Prof. Dawn Bowdish of McMaster University, has said that serology tests “are absolutely the gold standard for understanding the spread of this infection.” So, if both the PCR and serology tests are gold standard tests according to medical experts, albeit for different purposes, why not use both – from a simple and practical policy standpoint, to serve both purposes in Sri Lanka, and since both are needed. That is, both to diagnose patients and to track the virus spread. New serology tests are already being used in a number of countries, each priced at $10 (Rs. 2000, less than the PCR test cost of Rs. 6000), and able to give results in 20 minutes.

One more viewpoint on the matter of testing might be of particular relevance in the Sri Lankan context, with a tradition of doctors providing exceptionally good diagnosis in spite of limited resources for laboratory testing. Prof. David Fisman, Infectious Disease Epidemiologist and Physician at the University of Toronto, has suggested that given the newness of and the lack of information on Covid-19, ‘clinical case definitions’ should be used to identify Covid-19 cases where formal testing facilities are not sufficiently available. According to Dr. Fisman, clinical definitions were used during the SARS outbreak in Canada, and at the height of the current crisis in China, CT-scans were used in diagnosing Covid-19. Dr. Fisman has also suggested that in a pandemic situation such as this, every patient admitted to a hospital should be tested for Covid-19, along with healthcare providers. Testing of inmates in prisons, and other high-density dwellings and institutions would also make sense.

At this early stage of an epidemic caused by an etiologically little-known virus, the sampling for testing is invariably not random. Optimal sampling strategies have been developed for other disease epidemics that are both time-dependent and independent, and target both the vector (virus) and the host (human) populations. For now, in the case of the coronavirus, the rather crude metric of ‘tests per million’ appears to be the only guidance everywhere. Random sampling has been reported in Iceland, but the randomness assumption there is also being contested. In the light of all this and to get to practical matters, what could be the next steps in Sri Lanka?

Next Steps and Potential Slips

There is no further need to belabour the case, which is to implement both the PCR and the serological tests as rapidly as possible and as in many numbers as possible. Sri Lanka could learn from Vietnam, which has a low testing rate, about 1,200 tests per million people (and a total of 115,000 tests), but has aggressively carried out contact tracing and targeted ring-testing among the traced contacts to break the chain of transmission. The Sri Lankan government should support medical and health professionals to devise testing programs specific to each district, based on the experience so far and district-specific infection information, and implement them aggressively. There are medical faculties practically in every province and their resources should be leveraged to maximum benefit through co-ordination with the MRI and the Director General of Health Services.

It would also be helpful if the government could set up a proper professional forum where all the medical voices and opinions could be channeled and consulted without their having to find independent media outlets to express themselves. There is some media muttering that some medical voices are closer to the political powers than others. But that is inevitable and in itself should not be much of a concern, provided the scientific independence of the MRI and the administrative independence of the Director General of Health Services are not compromised.

To strike a personal note, I have found the silence of Dr. Tissa Vitarana in all of this somewhat puzzling. As onetime Director of the MRI, he was a highly respected medical scientist and was universally liked as a person, as some UNP Doctors used to say, in spite of his affiliations to the LSSP. His age should not be a factor, because everybody who is somebody in the current Administration is old. Dr. Vitarana is the only medical scientist who is politically associated with the current Administration. He is the Governor for the North Central Province and is also on the SLPP National List for the parliamentary election. And he could be a source of experience and wisdom in linking medical-scientific thinking and political decision making.

A ramped-up testing program and informed consultations based on test results will be critical in determining the next steps in coming out of the current curfew situations in the country. The virus is not going to disappear any time soon any where in the world, until an effective therapy or a successful vaccine is found. So, there cannot be a total relaxation of the current restrictive measures. In fact, it would be prudent to expect and prepare for restrictions and relaxation to alternatingly continue for rather long periods of time. And there are good practices to follow – from Vietnam, South Korea, Singapore and Taiwan.

Singapore is currently implementing a series of “stepping up measures” to deal with a second spike in the local transmission of the virus. Singapore calls the measures a “circuit breaker”, not a lockdown or a curfew, and they are being implemented with due preparation and prior notice to avoid public confusion and transport stampedes.  The measures will initially last a period of one month, which is calculated to cover two cycles of viral incubation. Additionally, modern supermarkets and traditional ‘wet markets’ will remain open and people will be allowed shop in orderly manner while maintaining minimum physical separation. These are not difficult measures and similar measures can be easily implemented in Sri Lanka. In Colombo, and other main cities, it should not be difficult to keep markets open and designate separate days of the week for households from different areas (e.g. by streets or ward) to do their shopping.  

Overall, the government faces three challenges: containing the virus; cushioning the economic fallouts; and ensuring the survival of constitutional politics. On the first, the government deserves all the credit that has been extended to it. Hopefully, it will keep up the good work, informed by sufficient test data and appropriately adopting good practices from East Asian countries. It is too soon to pass verdict on the second challenge. Even without the virus the government was in a deep hole and the virus has made it infinitely worse. Its first responsibility is to support employees and businesses who are involuntarily locked out of work, and this goes far beyond fulfilling the already established subsidy practices.

To that end, the government should look for immediate funding opportunities anywhere and everywhere, bilateral or multilateral. It could even send Chandrika Kumaratunga and Ranil Wickremesinghe as urgent emissaries to scour the world and not to return without foreign exchange. They could be more useful to the country from the outside than from within. Of course, they cannot emplane immediately, nor is physical travel really necessary with the new virus making virtual connections the new reality. Desperate times call for desperate measures, and no one is going to lose by working together in this crisis. Hopefully, I am not jinxing the possibility of a positive outcome for the country by publicly suggesting it.

The government should also forcefully nix lamebrained ideas emanating from within its ranks. Two have surfaced so far – one on (ab)using the EPF savings as a stimulus source, and the other to bring back import substitution from the long-ago dead. Neither seems to have found any traction, and hopefully both are still born, or dead on arrival. This is not to say that there is no room for new ideas, only they should not be lamebrained.

Worldwide food scarcity has been talked about even before the arrival of the virus, and its arrival makes it all the more urgent. Sri Lanka can and must re-energize its food production, but without raising barriers. It is a fact of Sri Lankan economic history that local food production has thrived only when there was no barrier at the customs, or checkpoints at district boundaries. One can be a socialist and doesn’t have to feel shy about saying this. As for new ideas, it would be worth for some in the government and the industry to explore the possibility of retooling the island’s industrial knowhow and technology in medical glove making and the garment industry to cater to the rising global demand for hospital gowns and other Personal Protection Equipment (PPE) for frontline healthcare providers. 

The third challenge is also the government’s Achilles’ heel, and where it can slip. The success here will be marked not by the extent of the SLPP’s victory at the next parliamentary election, whenever it comes, but by the extent to which President Gotabaya Rajapaksa and his Administration abide by constitutional norms in exercising executive power. A curfew without declaring emergency, avoiding emergency rule to avoid recalling parliament, and bankrolling off the national coffers, no matter how empty, without parliamentary approvals – are all jointly and severally beyond the pale in every direction. The President has the power and the option not to do any of this. And those who advise him to the contrary are not serving the President or the country well.

The latest in this vein is the missive by Presidential Secretary, Dr. P. B. Jayasundara, to Mahinda Deshapriya, Chairman of the Election Commission. The latter was ill-advised to start a public correspondence with the President on deciding a new date to hold the now postponed parliamentary election. Dr. Jayasundara, rather than elevating the discussion, has chosen to lower it by indulging in pettifogging and seriously indefensible polemics. He has lowered the office of the President. In the midst of a generational battle against a novel pathogen, President Gotabaya Rajapaksa deserves better from his Secretary. 

Coronavirus-02

 

My Thoughts on Coronavirus

My Thoughts on Coronavirus

Coronavirus coated particles are ONLY 120 nanometers.

It behaves like a enterovirus with hepatic phase before the respiratory complications (pneumonia)

Its asymmetric SINGLE RNA particles are much smaller and can assemble the infectivity and virulence even after one year (my belief) lay off.

In EVOLUTION RNA lasted pretty obstacles much better than DNA (double strand).

This EPIDEMIC is clearly lasts at lest two years.

1918-1919 Flu is the tell tale evidence but this is much better oriented to cause HAVOC.

I am not paranoid in this assessment.

Facemask has no place (smal viral RNA partcles can penetrate) but HAND WASHING several times a day is VITAL with or without soap.

Clean water is OUR current GOD.

Do not pollute with CHEMICAL HAZARDS (what they are spraying liberally now).

Coronavirous -03

 

Saturday, April 4, 2020

A Single Virus and a Humble Animal Send the Whole World into Lockdown

Reproduction

The author was our president for two terms, who retired gracefully from politics.

A Single Virus and a Humble Animal Send the Whole World into Lockdown

April 3, 2020, 6:35 pm

By Chandrika Bandaranaike Kumaratunga
The world has been attacked by the most widely spread pandemic the world has ever experienced.  It has had seismic effects on the entire world – almost no country has been spared from its terrifying repercussions.
We humans prided ourselves that we had conquered Mother Nature.  We indiscriminately destroyed her bountiful forests, thereby destroying large numbers of wild life or creating unnatural conditions in which humans were called upon to live in close proximity with wild animals.  We heartlessly polluted her rivers. Lakes and seas and the air that we breathe in the name of increased GDP and economic growth rates, regardless of the long-term dangers of all living beings.
We now find that we are knocked senseless by one single virus carried to us by a humble bat.  The entire world has been forced into lock-down.  We are only beginning to comprehend the possible outcome of this global viral attack on the national and global economy.  Not only would we have to re-think the whole paradigm of development, our concept of life and how we live it will change radically.
National Governments are acting individually in heroic attempts to contain the spread of the disease.  International and regional organisations too have gone into lockdown mode themselves, due perhaps to the unpreparedness of these organisaions for the present situation.  Nobody seems to have imagined that the shock and awe attack by a single virus could create such havoc, at such an unimaginable scale as the Corona Covid-19 virus has done.
The response of global and regional organisations has disappointed a lot of us, who believe in the necessity and power of international organisations to deal with issues that affect many or all countries of the world, by their very composition and objectives which we believe are to bring the world together in joint action, in times of peace and also when urgent action is required when emergencies arise.  We are disappointed that the global and regional organisations appear to be inept to deal with the present emergency.
It is evident that the first thing to do in this emergency is to control the spread of the disease, while medically caring for those who are infected by it.  I would call this, dealing with the result of a deep and serious problem.
It would be most constructive to study the origins of the problem – how and from where the present Covid virus came to infect the human being.
Innumerable theses are being expounded presently about the origins ohe virus, the manner in which it spread, and so on.  Even conspiracy theories are being circulated widely through social media.  At this time it is essential to base our understanding and explanations on established scientific facts and not various bits of somebody’s vivid imagination.  We must inquire if the theories that are put forward to us have any solid scientific basis.  If not, believing all this nonsense could lead to diverse political and human conflicts.
Serious research has demonstrated that as far back as 13 years ago in 2007, academics have raised alarm with regard to “wet markets” and the indiscriminate consumption of wild life in China, the Far East and countries in South America, as well as in many other countries worldwide.  Several papers by Chinese academic Cheng and others in their Paper written in 2007, gives a clear warning :
"Coronaviruses are well known to undergo genetic recombination, which may lead to new genotypes and outbreaks. The presence of a large reservoir of SARS-CoV-like viruses in horseshoe bats, together with the culture of eating exotic mammals in southern China, is a time bomb. The possibility of the reemergence of SARS and other novel viruses from animals or laboratories and therefore the need for preparedness should not be ignored."
Then Yi Fan and others in a Paper published in 2019 give an ominous prediction:
"Thus, it is highly likely that future SARS- or MERS-like coronavirus out​breaks will originate from bats, and there is an increased probability that this will occur in China."
Scientists at the forefront of infectious disease surveillance and research and epidemiologists have been warning their Governments and the whole world about the imminent danger of consuming wild animals as food.  It is unforgivable that the relative Governments, as well as international organisations, took no notice of this.
We are aware that the illegal international wildlife trade and the wet market trade of wild animals earns the Chinese economy as much as US$ 74 Billion per annum.  The short and medium term cost to Governments by the Covid 19 pandemic will likely be much more than fifty-fold of that value.
Didier Sicard, a French specialist of infectious diseases, working at the Institut Pasteur in Laos has noted that bats have harboured the Corona virus in their bodies since millions of years and can, in certain circumstances, disperse them to humans and other animals.  The destruction of virgin forests in Laos, for instance, has rendered it possible for bats, which normally live deep in the forests and caves, to begin to live close to human habitation and hence open up the flood-gates to spread the infection.  In this epidemic we know how dangerous contact could prove for the spread of the virus.
We are aware that the starting point of this pandemic is a public “wet market” in Wuhan where wild animals such as serpents, bats and others are kept crowded in cane baskets.  These animals are bought and consumed as delicacies.  This market is known to be crowded with animals and human beings and is not famous for its levels of cleanliness.  Hence, infected animals would have infected other animals, which in turn would have infected people.
In a seminal article written by Tara Schlegel,* she expresses surprise that our countries seem to be mainly interested in producing vaccines, treatments and re-animation which is admittedly the immediate requirement, but shows little or no interest with regard to the cause and the origins of the virus.  The problem is further compounded by our knowledge that wild animals are effectively at the origin of a large number of epidemics since the beginning of time – the Plague, HIV, bird flu, Ebola are some recent examples.  
It is said that bats carry some 30-odd corona-type viruses.  
Snakes of all types live in the same caves and forests inhabited by bats.  When bats die in their caves they are eaten by serpents, which thereby become infected by the virus.  It is also thoughts that other animals/insects such as ants could be infected.  All this makes it evident that extensive research needs to be undertaken to study the entire chain of contamination caused by the bats.
The study of the relationship between the Covid-9 carrying bats and their contamination of serpents, in addition to ants and other animals which live in close proximity of the serpents, and how they could infect humans becomes essential if we are to understand how humans contract the virus and how we could control the spread of it.
The accelerated destruction of forest cover in Indo-China and China could be a certain cause of bringing human habitation unnaturally close to that of wild animals and thereby promoting the propagation of various diseases, including the Covid Virus.

URGENT GLOBAL ACTION REQUIRED
1.    Global action appears essential for joint programmes of research to study the origins and the chain of transmission of the virus, about which I have given details above.  This implies in-depth study of the animals which transmit this virus.  It would also imply the study of other animals such as rats, which are known to transmit the bacteria that causes plague.
*Tara Schlegel, Radio France.
2.    International action to bring laws to forbid national and international trade in wild animals and the total ban of “wet markets” in every country of the world.  It may become necessary to create International/Regional institutions to monitor the implementation of these laws, with independent inspectors to survey the implementation at local level.
3.    To promote close and effective co-operation between Governments under the aegis of International Organisations such as the UNO and regional  organizations and the WHO, for the development of medical treatment, preventive vaccines, etc. to fight the covid-19 virus.  The WHO will have to re-structure itself to meet the present emergency, as well as other similar health emergencies which seem imminent in our world today.
To achieve this, it is proposed that an international meeting of a selected number of former and present leaders of Government, together with experts, be summoned without delay, with the objective of formulating policies and a programme of action.  This process could be co-ordinated and/or led by the UNO.

Coronavirus-04

 

Thursday, March 26, 2020

Hold On for a Minute

Hold On for a Minute

I am going to be blunt in expressing my views here some based on empirical, some scientific and some gut feelings.

There is a lot we do not know about this pandemic and the herd immunity is well below the potential for containment and my guess work is that once it enters, India and Africa, just like AIDS it becomes a global phenomenon which the W.H.O. won’t be able to predict its final outcome (in developing countries in particular) in the near future.

What we Know

1. Its size is 120 nanometers.

2. Its a RNA dependent RNA polymerase.

3. It behaves like an enteric virus (that is why the delay of 10 days as opposed to 3 to 5 days of Flu virus).

4. It is a large protein with a protective coat hijacked from the host cells.

5. The primary host cell is unknown and my guess is the hepatocyte or perhaps macrophage (provided the macrophage has a receptor protein to engulf it).

 

6. It hijacks the ribosomal protein factory of the host cell (most likely the hepatocyte where most of body proteins are manufactured).

7. It can mutate on its own will.

Why?

It does not need DNA mechanism of the host cell.

8. It can mimic (mimicry) the host cell’s proteins for its own survival and may bypass the host immune reaction to its own advantage and perhaps may even cause autoimmunity problem in some individuals.

9. It has its own protease enzyme to dissect the host protein and may even use the host cell protease for its own advantage.

10. Viral pneumonia is a process when antigen excess over antibody may cause an excess of inflammatory response (macrophage pushed to second place -leukocte response is enhanced- to clear the debries) and an alarming exudate into the lung alveoli.

This is where the ventilators come handy to push the negative pressure created (usually higher pressure created by the surfactant in the alveoli lining mitigates the exudation of fluids) in the alveoli back to manageable proportion by artificial means and allow macrophages to clean up the mess in the lung.

The premature babies lacks the surfactant and adults with chronic cardio-pulmonary disease have more devastating outcome.

What can be done?

1. Treat it like an enerovirus with vigorous hand washing and no touch technique (do not touch possible contaminated surfaces in public places).

2. Self discipline and home isolation over long period of time and physical distancing.

3. Social interaction with a land phone.

4. Cellphone (do not share) is a carrier and there are now UV light disinfectant cases already in the market.

5. Stop all contact sports (close gymnasiums) and use not towels but disposable paper towels.

6. Avoid all unnecessary travel especially by airlines.

7. Wearing a mask is optional (to hand washing) for normal uninfected but mandatory for sick individuals and health care personnel (save the masks for them).

8. Home gardening including vegetables is an option we have neglected (why visit the market for ginger and turmeric).

9. Coriander, Perumkayam and Khohoma are vital local remedies.

10. Hang a Khohomba (an old tradition) leave branch on the front and the back door if someone incubating the disease is domesticated.

Reproduction from New England Journal of Medicine

At the beginning of the epidemic, the estimated basic reproductive number (R₀) was 2.38 and the percentage of undocumented infections was 86.0%. Undocumented infections were estimated to cause 86.2% of all infections. Later in the epidemic and with augmented testing, the proportion of undocumented infections fell to 35%, and the R₀ dropped to 1.36 and then to 0.99 as restrictions on geographic movement tightened.

Comment

To end an epidemic, R₀ must be kept below 1.0 in a sustained fashion. Mathematical modeling of epidemics is fraught with uncertainty given its reliance on numerous assumptions that sometimes turn out to be faulty. However, this study's rigorous modeling data underscore that drastic, prolonged geographic mobility restrictions are needed to contain the SARS-CoV-2 pandemic.

Many countries are currently paying this high societal cost while awaiting the advent of an effective vaccine.

Coronavirus-05

 Flip Side of Coronavirus Pandemic

There are lot of positive signs for Ceylonese barring the difficulties for the people who are on hand to mouth existence.

They call the private and public transport, the Eda-Wela Tours.

This applies to Three Wheeler drivers who resist using a meter for the miles traveled before charging.

Most of these three wheeler drivers are government’s spoke-persons on wheels.

They haven’t got anything substantial for ages but do work as slaves to the government machinery in faith but not in conviction.

1. Number one point is no election round the corner.

What a saving?

2. There are currently no parliamentary members or provincial council members causing huge sum to be saved by the treasury.

What a saving?

3. Health ministry can perform admirably to take a lead without ministers and state ministers looking over their shoulders.

If a elected government was in power with so many meetings in every street corner of the country the virus that is in the coastal belt now would have come to the center of the country.

We are relatively free in the center of the country including Kandy since the railways are not running.

Railways would have carried the virus to the Estate Sector where our vital Tea Economy rests.

4. We do not have to listen to the warped politics of Vasu, Dinesh, Bandula and Werawansa for a considerable length of time.

5. I think five ministers in total including Prime Minister is enough to run the country in peace time and war time (Coronavirus).

6. The Coronovirus has shown that though, it is small in nanometers but very powerful in impact.

7. A small government could be more efficient (does not mean a military dictatorship is the alternative. Our military is huge and expensive to run in peace time and using them to packet dry ration is damning. I have no grouse they are helping -directing rather than slaves- the police for proper distribution without pilfering).

8. I think total shutdown of the parliament until the virus spread is under full control is mandatory (saving made by shutdown should be delivered to the health care sector).
The parliamentary members may become a vehicle of spread in no time.

It has happened in Senate and Congress (members) in USA.

9. Of course The election Commissioner and his panel can go into sleep gear for some time.

10. Shutting down TV (they have only Coronavirus news) and leaving the Radio Stations to function is more meaningful (in all three languages).

11. Last but not least canceling the New Year Celebrations would damp down the spread of the virus.
It is the Chinese New Year craze that made it become a pandemic from a tiny epidemic. 

Coronavirus-06

 

Update on Coronavirus

Update on Coronavirus

This is in response to a few of my friends.

In other words if one takes a vegetarian diet at least in old age without beef is actually the best way of healthy living.

1. This virus originated in China and those incubating the disease landed in Singapore and entered Europe most likely by Singapore Airline or its subsidiary Airline.

2. Airline pilots and cabin crews, incubating this disease had been traveling all over world before the travel restriction, including USA.

3. It is very difficult to quarantine a patient in a plane in pressurized atmosphere and it is very common to catch a flu on a long haul flight.

4. Few airlines going bust due to credit crisis is welcome and most of the charter flights, the quality of service plummeted but the their income went up exponentially.

5. My last flight by Singapore airline was hopeless and I could not get a extra glass of water from the cabin crew.

It was the young passenger who was seated next to me who came to my rescue and offered me a glass of water.

6. China for its own part tried to suppress the information and one of its doctors who tried to exposed the secrecy succumbed to the virus.

7. Now 7 doctors in USA had died and another 20 infected due to poor coordination of public health information of and its potential danger.

8. Now even Africa is affected (most likely India, too) due to lack of testing agents.

9. In Ceylon they allowed the Chinese travelers free entry and they are allowed (not Ceylonese passport officers) to process their own passports- (nowhere in the world, there is a scheme like this) and only quarantines plane load of our students.

10, Our health officers are not divulging the true facts (bungling by the present governments) about “how late in handling’ the quarantine issue.

11.Closing the schools and universities came too late and I bet our election commissioner will hold elections in spite of the risks involved to the voter and public who would not bother voting.

12. Most of our sports facilities (schools,too) do not have proper washrooms and toilets and the sharing the towel and water bottle, habit of J.V.P. camaraderie is a high risk in this country.

13. In my opinion a face mask is a big risk both of collecting a viral load and disposing (burning) after use DUE to relatively big size of the virus which is 120 nm. 

A high quality face masks are not available even in our surgical theaters, not allowing 15 to 20 nm (that is the size of the small branches of the bronchial tree) particles that penetrate the virtual lung barrier.

14. Most optimistic preventive measure is by washing of hands up to the elbow with soap and water. (The mounting and standing bars of buses and staircase elevators are never cleaned)

14. Not to share cutlery and utensils even at home (how many can afford).

15. Stay at home with early signs of any infection (it is too late in most infections, disease is spread during the incubation period which is six weeks in infective hepatitis).

16. Take Vitamin C (cheaper than fruits) as a habit.

17. No western medicine available but there are lot of Aurvedic remedies.

18. Coriander seeds as a drink and coriander leaves as a curry.

19. Garlic, Ginger, Lime, Lemon, Tumeric (not Wada Kaha) and Vinegar.

20. If you can find Perumkayam!

21. In other words if one takes a vegetarian diet at least in old age without beef is actually the best way of healthy living.

22. Egg is allowed as a default vitamin store.

Below is a reproduction from Wikipedia and I want to make few comments even though, I am not a virologist.

There are roughly three types of viruses, DNA, RNA and Retrovirus (AIDS is an example).

Coronavirus is a RNA virus that hijacks the cell protein production factory the Ribosomes with its own RNA dependent RNA polymerase.

1. It hijacks cell protein factory the ribosome

2. Its receptor is cells own protein component.

3. CD (Cell Definition) classification is yet not well defined.

4. What cells have this CD specificity is unknown.

5. It uses a poly-protein of its own creation and a protease to dissect its own protein components. That leads to relative protein deficiency for cells that are affected.

6.We do not know the homology of the viral protein with the normal cell proteins.

7. If the homology is great the body won’t mount an active antibody production to avoid autoimmunity.

8. Whether it causes protein deficiency and autoimmunity needs to be worked out.

9. My belief is that it is an animal virus that causes no problem for in the animal kingdom but once it enters the humans population it can create havoc.

10. If it originated from a bird avoid eating chicken (starve the virus of its base protein hijacking ability) similarly if it originated from pigs (bigger animal) avoid eating pork and beef (to starve the virus of is base protein hijacking ability).

11. If it originated from bats (most likely), I do not have any worthwhile suggestion to contribute.

12. It is better to revert to vegetable protein like ToFu (amino acid composition is different to animal protein) instead of animal proteins.

13. My prediction is because this virus has a RNA dependent RNA polymerase which can mutate at its own will the epidemic will last at least a decade until the herd immunity takes its toll but by then another virus more potent than this will emerge from a viral laboratory that do do not have rigid protocols and closely not monitored by a regulatory authority.

14. I believe all developed countries and China may be developing biological weapons secretly and science (biological) may be killed by its own science initiative.

Regulation is mandatory!

Coronavirus Morphology

Coronaviruses are large pleomorphic spherical particles with bulbous surface projections.
The diameter of the virus particles is around 120 nm.
The envelope of the virus in electron micrographs appears as a distinct pair of electron dense shells.
The viral envelope consists of a lipid bilayer where the membrane (M), envelope (E) and spike (S) structural proteins are anchored.
A subset of coronaviruses (specifically the members of Betacoronavirus subgroup A) also have a shorter spike-like surface protein called hemagglutinin esterase (HE).
Inside the envelope, there is the nucleocapsid, which is formed from multiple copies of the nucleocapsid (N) protein, which are bound to the positive-sense single-stranded RNA genome in a continuous beads-on-a-string type conformation.The genome size for coronaviruses ranges from approximately 27 to 34 kilobases.
The lipid bilayer envelope, membrane proteins, and nucleocapsid protect the virus when it is outside the host cell.

Coronavirus Replication

Infection begins when the virus enters the host organism and the spike protein attaches to its complementary host cell receptor. After attachment, a protease of the host cell cleaves and activates the receptor-attached spike protein. Depending on the host cell protease available, cleavage and activation allows cell entry through endocytosis or direct fusion of the viral envelop with the host membrane.
On entry into the host cell, the virus particle is uncoated, and its genome enters the cell cytoplasm.[
The coronavirus RNA genome has a 5′ methylated cap and a 3′ polyadenylated tail, which allows the RNA to attach to the host cell's ribosome for translation.
The host ribosome translates the initial overlapping open reading frame of the virus genome and forms a long polyprotein.
The polyprotein has its own proteases which cleave the polyprotein into multiple nonstructural proteins.
A number of the nonstructural proteins coalesce to form a multi-protein replicase-transcriptase complex (RTC).
The main replicase-transcriptase protein is the RNA-dependent RNA polymerase (RdRp).
It is directly involved in the replication and transcription of RNA from an RNA strand. The other nonstructural proteins in the complex assist in the replication and transcription process. The exoribonuclease non-structural protein for instance provides extra fidelity to replication by providing a proofreading function which the RNA-dependent RNA polymerase lacks.
One of the main functions of the complex is to replicate the viral genome. RdRp directly mediates the synthesis of negative-sense genomic RNA from the positive-sense genomic RNA. This is followed by the replication of positive-sense genomic RNA from the negative-sense genomic RNA.
The other important function of the complex is to transcribe the viral genome. RdRp directly mediates the synthesis of negative-sense subgenomic RNA molecules from the positive-sense genomic RNA. This is followed by the transcription of these negative-sense subgenomic RNA molecules to their corresponding positive-sense mRNAs.
The replicated positive-sense genomic RNA becomes the genome of the progeny viruses.
The mRNAs are gene transcripts of the last third of the virus genome after the initial overlapping reading frame. These mRNAs are translated by the host's ribosomes into the structural proteins and a number of accessory proteins.
RNA translation occurs inside the endoplasmic reticulum. The viral structural proteins S, E, and M move along the secretory pathway into the Golgi intermediate compartment. There, the M proteins direct most protein-protein interactions required for assembly of viruses following its binding to the nucleocapsid.
Progeny viruses are then released from the host cell by exocytosis through secretory vesicles.