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Pandemic! Pandemic?

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By Dr. F.E. Dias

An epidemic affects a high proportion of a population at the same time, and with respect to disease, it means an outbreak that spreads quickly and regionally affects a disproportionate number of people. Pandemics are epidemics that spread across wide geographical areas such as nations and continents. It should be a matter of interest to us that, according to information prevailing and incessant regarding the pandemic, we are said to be in the middle of, the proportion of, shall we say patients, as routinely identified via PCR tests, who show no symptoms of COVID-19 greatly outweigh those that do.

Preamble

Let us first understand what we are talking about. Coronaviruses are a family (Coronaviridae) of viruses that can cause the common cold, SARS (attributed to SARS-CoV) and MERS (attributed to MERS-CoV), the latter two being qualified as Severe Acute and Middle East respectively. The respiratory malady we refer to as the common cold can also be caused by other virus types including rhinoviruses, influenza viruses, adenoviruses and several others, often in combination, with about 200 causal viral variants identified thus far, and many causative agents not yet identified.

Whereas for what is called the common cold there is no clear link between pathogen and disease, the beta-coronavirus named SARS-CoV-2, whatever its origins, is specified as the cause of the coronavirus disease 2019 or COVID-19, common symptoms of which are fever, cough, fatigue and many others such as shortness of breath, muscle ache, runny nose and nausea to name a few, symptoms similar to those of the common cold, influenza and other febrile diseases and allergy response. The virus usually spreads via respiratory droplets released from a carrier individual, hence the muzzles we wear while the dogs stare at us pondering at the turning of tables. So, SARS-CoV-2 is our virus and COVID-19 is the associated series of clinical symptoms, called the disease.

Detection

What about the testing to find out whether the symptoms you have can be attributed to SARS-CoV-2? There are three pertinent types of tests. One is the nucleic acid amplification via polymerase chain reaction (PCR) test which is used today with the claim that it diagnoses the disease. That is, one is given to understand that it says whether you, even when asymptomatic, are infected and thereby contagious. The other two are antigen and antibody tests. Let us understand.

Antibodies, also known as immunoglobulins, are proteins produced by the B-lymphocytes in the immune system to latch on to foreign substances and consequently remove them from the body, thereby protecting from the potent harm that the foreign substance could have caused. Such foreign substances as recognised by the antibodies are called antigens, which could be toxins or components of pathogens such as the spike glycoproteins of the Coronavirus that help it to enter the host. Detection of the specific antibodies in serum does indicate that the specific antigen has entered the body but since the production of antibodies may occur days or weeks after the antigen has entered and may continue its presence for a significant period after the antigen no longer poses a threat, it does not indicate that you are at that moment likely to develop disease or to infect others. It is not diagnostic by that understanding but will be useful for assessing the durability of vaccine response or of naturally acquired immunity.

Antigens then are substances capable of eliciting an immune response. The antigen test – which is familiar to us as, the rapid test that provides a result in 15 minutes, detects the aforementioned surface protein fragments specific to the virus. While other factors such as the test kit source and competency of swabber and tester do matter, these tests provide a positive result usually when there is high or near-peak viral load. By this point, the symptoms may have begun to appear, and the individual is most contagious. It is fast, cheap and fairly simple, but could be considered as a test for infectiousness than one for infection.

PCR

The polymerase chain reaction is used to replicate a segment of DNA so that quantity sufficient for detection and analysis is produced. The SARS-CoV-2 virus has single-stranded RNA as its genetic material. Reverse transcription (RT) converts RNA into DNA. In each cycle of replication, the quantity of the gene sequence of interest is doubled so that after 40 replication cycles, a single sequence of nucleic acid would have multiplied a trillion times, that is a million of millions. The technique was developed by Dr. Kary Mullis in the eighties and he received the Nobel prize for chemistry in 1993 on account of its vast applications in genetics, microbiology, forensic science and medicine. Even Hollywood used PCR on fossilised DNA to revive and populate the Jurassic Park!

But how is the technique connected to the disease? The protocol published in January 2020 by the WHO, for public health laboratories to use in the detection of SARS-CoV-2, is based on real-time RT-PCR. A paper describing this methodology, now referred to as the Corman-Drosten paper, was subsequently submitted to the journal Eurosurveillance. It was published within 24 hours of submission, raising questions regarding the peer-review process, and two of the authors were members of the editorial board of the same journal. The protocol was consequently used in ~70 percent of tests globally and by a hundred governments and is called the gold standard for COVID-19 testing. We know it as the PCR test which if it turns out positive makes you a patient, understood to be infected and contagious, and all that follows.

The PCR test as conducted as per WHO guidelines is binary qualitative in that it returns a positive or negative result after the pre-decided number of replication cycles have been performed. The number of cycles is known as the positivity threshold or cycle threshold (cT) and is the determinant of sensitivity. The Corman-Drosten protocol does not define the threshold but appears to suggest the use of 45 replications.

Independent analyses of PCR test results against the inoculation and culture of the same samples showed that for 35 replication cycles, less than three percent produced positive cultures. That is, for a cT of 35, 97 percent of PCR test results that came out positive were, in fact, false positives. On this basis, 97 percent of ‘COVID-19 cases’ were not infected with SARS-CoV-2. For cT values above 35, the data approaches the asymptote and indicates 100 percent false positives. Most lab reports do not indicate the cT used in their test but 30 to 45 is usual.

In November 2020, a group of scientists formally pointed out flaws in the Corman-Drosten protocol. Apart from not defining the cT, there were factors such as atypically high concentrations of primer (replication initiators) that cause increased unspecific binding and product amplication, substantial variability and error in test process design that could lead, inter alia, to other Coronaviruses being detected or for residual fragments of viral RNA to be sufficient to indicate the presence of the whole virus. Such residuals may quite well be indications of a battle won by the immune system against last week’s common cold. Also, the genetic code considered for the development of the test protocol was based on theoretical or in silico sequences supplied by a Chinese laboratory since the authors at that time did not have access to infectious or inactivated SARS-CoV-2 or its isolated genomic RNA.

In January 2021, reportedly one hour after the Biden inauguration, the WHO issued a notice urging caution in the interpretation of PCR test results, stating that their protocol is merely an aid for diagnosis and that assay specifics and clinical observations need to be considered. Since it followed that it was no longer the gold standard for diagnosis, a person who tested positive on a flawed PCR protocol conducted with a meaninglessly high cT would not thereby be classified as infected or having the disease. Since then, the COVID-19 numbers have substantially reduced, at least in the USA. Eventually, in July 2021, the CDC announced that it has requested the FDA to withdraw its request for emergency use authorization of this PCR test as a diagnostic tool for the detection of SARS-CoV-2, admitting that it cannot distinguish between CoViD-19 and influenza.

Conclusion

There is the virus and its mutations. It causes illness, and complications and even death particularly when co-morbidities pre-exist. Precautions need to be taken to protect from infection, especially among those with weaker immune systems such as the elderly. Action needs to be pursued to eradicate the pathogen and even to prevent others being developed. And yet, the world has completed a revolution around the sun since the WHO declared COVID-19 to be a pandemic in March 2020. The world has undergone a revolution as a consequence of this declaration and is still reeling from it. The question is, however, whether the pandemic was indeed a pandemic after all, at least until the vaccination campaigns began.

Corman-Drosten paper – https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.3.2000045

WHO adoption – Protocol V2 (who.int)

WHO original – Diagnostic testing for SARS-CoV-2 (who.int)

WHO change – WHO Information Notice for IVD Users 2020/05

CDC withdrawal – https://www.cdc.gov/csels/dls/locs/2021/07-21-2021-lab-alert-Changes_CDC_RT-PCR_SARS-CoV-2_Testing_1.html



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NASA’s Epic Flight, Trump’s Epic Fumble and Asian Dilemmas

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Epic Crew (L-R): Jeremy Hansen, Victor Glover, Reid Wiseman Christina and Christina Koch

Three hours after the spectacular Artemis II flight launch in Florida, US President Donald Trump delivered a forlorn speech from Washington. Thirty three days after starting the war against Iran as Epic Fury, the President demonstrated on national and global televisions the Epic Fumble he has made out of his Middle East ‘excursion’. It was an April Fool’s Day speech, 20 minutes of incoherent rambling with the President looking bored, confused, disengaged and dispirited. He left no one wiser about what will come next, let alone what he might do next.

There was more to April Fool’s Day this year in that it brought out the nation’s good, bad and the ugly, all in a day’s swoop. The good was the Artemis II flight carrying astronauts farther from the Earth’s orbit and closer to the moon for the first time in over 50 years. The mission is a precursor for future flights and will test the performance of a new spacecraft, gather new understanding of human conditioning, and extend the boundaries of lunar science. It is a testament to humankind being able to make steady progress in science and technology at one end of a hopelessly uneven world, while poverty, bigotry and belligerence simmer violently at the other end.

Terrible Trump

The four Artemis II astronauts, three Americans, Reid Wiseman, Victor Glover, and Christina Koch, and one Canadian, Jeremy Hansen, are also symptomatic of the endurance of America’s inclusive goodness in spite of efforts by the Trump Administration to snuff the nation’s fledgling DEI (Diversity, Equity and Inclusion) ethos. To wit, of the four astronauts, Victor Glover, a Caribbean American, is the first person of colour, Christina Koch the first woman, and Jeremy Hansen of Canada the first non-American – to fly this far beyond the earth’s orbit. All in spite of Trump’s watch.

Yet Trump managed to showcase his commitment to America’s ugliness, on the same day, by presenting himself at the Supreme Court hearing on the constitutionality of his most abominable Executive Order – to stop the American tradition of birthright citizenship. He keeps posting that America is Stupid in being the only country in the world that grants citizenship at birth to everyone born in America, regardless of the status of their parents, except the children of foreign diplomats or members of an occupying enemy force. In fact, there are 32 other countries in the world that grant birthright citizenship, a majority of them in the Americas indicating the continent’s history as a magnet for migrants ever since Christopher Columbus discovered it for the rest of the world.

And birthright citizenship in the US is enshrined in the constitution by the 14th Amendment, supplemented by subsequent legislation and reinforced by a century and a half of case law. Trump wants to reverse that. Thus far and no further was the message from the court at the hearing. A decision is expected in June and the legal betting is whether it would be a 7-2 or 8-1 rebuke for Trump. In a telling exchange during the hearing, when the government’s Solicitor General John Sauer quite sillily dramatized that “we’re in new world now … where eight billion people are one plane ride way from having a child who’s a US citizen,” Chief Justice John Roberts quietly dismissed him: “Well, it’s a new world. It’s the same Constitution!”

Trump’s terrible ‘bad’ is of course the war that he started in the Middle East and doesn’t know how to end it. Margaret MacMillan, acclaimed World War I historian and a great grand daughter of World War I British Prime Minister Lloyd George from Wales, has compared Trump’s current war to the origins of the First World War. Just as in 1914, small Serbia had pulled the bigger Russia into a war that was not in Russia’s interest, so too have Netanyahu and Israel have pulled Trump and America into the current war against Iran. World War I that started in August, 2014 was expected to be over before Christmas, but it went on till November, 2018. Weak leaders start wars, says MacMillan, but “they don’t have a clear idea of how they are going to end.”

There are also geopolitical and national-political differences between the 1910s and 2020s. America’s traditional allies have steadfastly refused to join Trump’s war. And Trump is under immense pressure at home not to extend the war. This is one American war that has been unpopular from day one. The cost of military operations at as high as two billion dollars a day is anathema to the people who are aggravated by rising prices directly because of the war. Trump’s own mental acuity and the abilities of his cabinet Secretaries are openly under question. There are swirling allegations of military contract profiteering and selective defense investments – one involving Secretary of War Pete Hegseth.

Trump’s Administration is coming apart with sharp internal divisions over the war and government paralysis on domestic matters. There are growing signs of disarray – with Trump firing his Attorney General for not being effective prosecuting his political enemies and Secretary Hegseth ordering early retirement for Army Chief of Staff Randy George. In America’s non-parliamentary presidential system, Trump is allowed to run his own forum where he lies daily without instant challenger or contradiction, and it is impossible to get rid of his government by that simple device called no confidence motion.

Asian Dilemmas

Howsoever the current will last or end, what is clear is that its economic consequences are not going to disappear soon. Iran’s choke on the Strait of Hormuz has affected not only the supply and prices of oil and natural gas but a family of other products from fertilizers to medicines to semiconductors. The barrel price of oil has risen from $70 before the war to over $100 now. After Trump’s speech on April 1, oil prices rose and stock prices fell. The higher prices have come to stay and even if they start going down they are not likely to go down to prewar levels.

There are warnings that with high prices, low growth and unemployment, the global economy is believed to be in for a stagflation shock like in the 1970s. Even if the war were to end sooner than a lot later, the economic setbacks will not be reversed easily or quickly. Supplies alone will take time to get back into routine, and it will even take longer time for production in the Gulf countries to get back to speed. Not only imports, but even export trading and exports to Middle East countries will be impacted. The future of South Asians employed in the Middle East is also at stake.

In 1980, President Carter floated the Carter Doctrine that the US would use military force to ensure the free flow of oil through the Strait of Hormuz. Trump is now upending that doctrine – first by misusing America’s military force against Iran and provoking the strait’s closure, and then claiming that keeping the strait open is not America’s business. Ever selfish and transactional, Trump’s argument is that America is now a net exporter of oil and is no longer dependent on Middle East oil.

To fill in the void, and perhaps responding to Trump’s call to “build up some delayed courage,” UK has hosted a virtual meeting of about 40 countries to discuss modalities for reopening the Strait of Hormuz. US was not one of them. While Downing Street has not released a full list of attendees, European countries, some Gulf countries, Canada, Australia, Japan and India reportedly attended the meeting. Which other Asian countries attended the meeting is not known.

British Foreign Secretary Yvette Cooper has blamed Iran for “hijacking” an international shipping route to “hold the global economy hostage,” while insisting that the British initiative is “not based on any other country’s priority or anything in terms of the US or other countries”. French President Emmanuel Macron now visiting South Korea has emphasized any resolution “can only be done in concert with Iran. So, first and foremost, there must be a ceasefire and a resumption of negotiations.”

Prior to the British initiative focussed on the Strait of Hormuz, Egypt, Pakistan and Türkiye have been playing a backdoor intermediary role to facilitate communications between the US and Iran. Trump as usual magnified this backroom channel as serious talks initiated by Iran’s ‘new regime’, and Trump’s claims were promptly rejected by Iran. There were speculations that Pakistan would host a direct meeting between US Vice President JD Vance and an Iranian representative in Islamabad. So far, only the foreign ministers of Egypt, Pakistan, Saudi Arabia and Türkiye have met in Islamabad, and Pakistan’s Foreign Minister Ishaq Dar flew to Beijing to brief his Chinese counterpart, Wang Yi, of Pakistan’s diplomatic efforts.

The Beijing visit produced a five-point initiative calling for a ceasefire, the opening of the Strait of Hormuz and diplomacy instead of escalation. The five-point pathway seems a follow up to the 15-point demand that the US sent to Iran through the three Samaritan intermediaries which Iran rejected as they did not include any of Iran’s priorities. The state of these mediating efforts are now unclear after President Trump’s April Fool’s Day rambling. In fairness, Pakistan’s Ministry of Foreign Affairs has announced that his country intends to keep ‘nudging’ the US and Iran towards resuming negotiations and ending the war.

While these efforts are welcome and deserve everyone’s best wishes, they have also led to what BBC has called the “chatter in Delhi” – “is India being sidelined” by Pakistan’s intermediary efforts? Indian Foreign Minister Jaishankar’s rather undiplomatic characterization of Pakistan’s role as “dalali” (brokerage) provoked immediate denunciation in Islamabad, while Indian opposition parties are blaming the Modi Government’s foreign policy stances as an “embarrassment” to India’s stature.

The larger view is that while it is Asia that is most impacted by the closure of Hormuz, with Singapore’s Foreign Affairs Minister Vivian Balakrishnan calling it an “Asian crisis”, Asia has no leverage in the matter and Asian countries have to make special arrangements with Iran to let their ships navigate through the Strait of Hormuz. There is no pathway for co-ordinated action. China is still significant but not consequentially effective. India’s all-alignment foreign policy has made it less significant and more vulnerable in the current crisis. And Pakistan has opened a third dimension to Asia’s dilemmas.

In the circumstances, it is fair to say that Sri Lanka is the most politically stable country among its South Asian neighbours. Put another way, Sri Lanka has a remarkably consensual and uncontentious government in comparison to the old governments in India and Pakistan, and even the new government in Bangladesh. But that may not be saying much unless the NPP government proves itself to be sufficiently competent, and uses the political stability and the general goodwill it is still enjoying, to put the country’s economic department in order. More on that later.

by Rajan Philips

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Ranjith Siyambalapitiya turns custodian of a rare living collection

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Siyambalapitiya’s ancsetral house built on 1923 at Vendala

From Parliament to Fruit Grove:

After more than two decades in politics, rising to the positions of Cabinet Minister and Deputy Speaker of Parliament, Ranjith Siyambalapitiya has turned his attention to a markedly different arena — one far removed from parliamentary debate and political intrigue.

Today, Siyambalapitiya spends much of his time tending to a sprawling 15-acre home garden at Vendala in Karawanella, near Ruwanwella, nurturing what has gradually evolved into one of the most remarkable private fruit collections in the country.

Situated in Sri Lanka’s Wet Zone Low Country agro-ecological region (WL2), Ruwanwella lies at an elevation of roughly 100–200 metres above sea level. Deep red-yellow podzolic soils, annual rainfall exceeding 2,500 millimetres, and a warm humid tropical climate combine to create conditions that make the region one of the richest areas in the island for fruit tree diversity.

Within this favourable ecological setting, Siyambalapitiya has become what may best be described as a custodian of a living collection—a fruit grove that now contains around 554 fruit trees and vines, many of them rare or seldom seen in contemporary agriculture.

Of these, 448 varieties have already been properly identified and documented with the assistance of agriculturist Dr. Suba Heenkenda, a retired expert of the Department of Agriculture. Together they have undertaken the painstaking task of cataloguing the plants by their botanical names, common Sinhala names, and the names used in ancient Ayurvedic and indigenous medical texts, assigning each species a unique identification number.

According to Siyambalapitiya, the Vendala estate is possibly the only single location in Sri Lanka where such a large number of fruit varieties—particularly rare and underutilized species—are maintained within one property.

“This garden came down to me through my grandfather, grandmother, mother and father,” he says. “It is a place shaped by three generations.”

The estate, he explains, began as a traditional home garden where crops such as tea, coconut and rubber were cultivated alongside fruit trees planted by family members over decades. Over time, however, it evolved into something much larger: a carefully nurtured grove preserving both common and obscure fruit species.

Siyambalapitiya recalls with affection one of the oldest trees in the garden—a honey-jack tree known locally as “Lokumänike’s Rata Kos Gaha.”

The story behind it has become part of family lore. According to village elders, his grandmother had brought home the sapling after visiting the Colombo Grand Exhibition in 1952 many decades ago and planted it near the house.

The tree soon gained fame in the village. Its tender jackfruit proved ideal for curry and mallum, while the ripe fruit was renowned for its sweetness.

“Ripe jackfruit from this tree tastes like honey itself,” Siyambalapitiya says. “Even the seeds are full of flour and can be eaten throughout the year.”

Yet age has not spared the venerable tree. It now shows signs of disease, and Siyambalapitiya and his staff have had to treat old wounds and monitor unusual bark damage.

“Once lightning struck it,” he recalls. “The largest branch began to die. Saving the tree required what I would call a kind of surgical operation.”

Such care, he says, reflects the deep attachment he feels toward the collection.

His fascination with fruit trees began in childhood. While attending Royal College in Colombo and living in a boarding house he disliked, Siyambalapitiya would insist that the family procure new fruit saplings for him to plant during his weekend visits home.

“That was the only ‘price’ I demanded for going to school,” he laughs.

Over the years the collection expanded steadily as he encountered new plants in forests, nurseries, and rural landscapes across the island.

The result today is a grove that includes traditional Sri Lankan fruit species, underutilized native varieties, forest fruits, and plants introduced from overseas.

Some species originate in Arabian deserts, while others thrive naturally in cooler climates such as Europe. Certain plants require greenhouse-like conditions, while others are hardy forest trees.

Managing such diversity is no easy task.

“One plant asks for rain, another asks for cold, and yet another prefers heat,” Siyambalapitiya explains. “Too much rain makes some sick, too much sun troubles others. The older trees overshadow the younger ones. You cannot feed or medicate them all in the same way.”

He compares the task to caring for a household filled with people from many nations and ages—each with different needs.

Despite the challenges, he believes the effort is worthwhile, particularly because many of the trees are native species that have become increasingly rare.

“If things continue as they are, some of these plants may disappear from our lives,” he warns.

To preserve knowledge about them, Siyambalapitiya is preparing to launch a book titled “Mage Vendala Palathuru Arana” (My Vendala Fruit Grove), which serves as an introductory guide to the collection.

The book, scheduled for release on April 18 at the Vendala estate, will be attended by Ven. Dr. Kirinde Assaji Thera, Chief Incumbent of Gangaramaya Temple,

Uruwarige Wannila Aththo, the leader of the Indigenous Vedda Community,

a long-serving former employee who helped maintain the plantation, and Sunday Dhamma school students from the region, who will participate as guests of honour.

The publication will also mark Siyambalapitiya’s eighth book. Previously he authored seven works and wrote more than 500 weekly newspaper columns offering commentary on politics and current affairs.

While working on the fruit catalogue, he is simultaneously writing another volume reflecting on his 25-year political career, including his tenure as Deputy Finance Minister during Sri Lanka’s most severe economic crisis.

For Siyambalapitiya, however, the fruit grove represents more than a hobby or academic exercise.

“The fruit we enjoy is the result of a tree’s effort to reproduce,” he says. “Nature has given fruits their taste, fragrance and colour to attract us. All the tree asks in return is that its seeds be carried to new places.”

That simple cycle of life, he believes, has continued for tens of thousands of years.

“And those who love trees,” he adds, “are guardians of the world’s survival.”

by Saman Indrajith

Pix by Tharanga Ratnaweera

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Smoke Free Sweden calls out to WHO not to suggest nicotine alternatives

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It has been reported by the international advocacy initiative, ‘Smoke Free Sweden’ (‘SFS’) that many International health experts have begun criticizing the World Health Organization (WHO) for presenting safer nicotine alternatives rather than recognizing its role in accelerating decline in smoking.

As the world’s premier technical health agency, the WHO is empowered to support strategies that reduce morbidity and mortality even if they do not eliminate the underlying behaviour. Furthermore, it should base its guidance on evolving scientific knowledge, which includes comparative-risk assessments. Equating smoke-free nicotine alternatives with combustible cigarettes, is essentially putting lives at risk, according to the health experts contacted by SFS.

The warning follows recent WHO comments suggesting that vaping and other non-combustible nicotine products are driving tobacco use in Europe. This narrative ignores real-world evidence from countries like Sweden where access to safer alternatives has coincided with record low smoking rates.

A “Smoke-Free” status is defined as an adult daily smoking prevalence below 5% and Sweden is on the brink of officially achieving this milestone. This is clear proof that pragmatic harm-reduction policies work. Sweden’s success has been driven by adult smokers switching to lower-risk alternatives such as oral tobacco pouches (Snus), oral nicotine pouches and other non-combustible products.

“Vapes and pouches are helping to reduce risk, and Sweden’s smoke-free transition proves this,” said Dr Delon Human, leader of Smoke Free Sweden. “We should be celebrating policies that help smokers quit combustible tobacco, not spreading fear about the very tools that are accelerating the decline of cigarettes.”

It is further reported by health experts that conflating cigarettes with non-combustible alternatives risks deterring smokers from switching and could slow progress toward reducing tobacco-related disease.

Dr Human emphasized that youth protection and harm reduction are not mutually exclusive.

“It is critically important to safeguard against underage use, but this should be done by targeted, risk-proportionate regulation and proper enforcement, not by sacrificing the right of adults to access products that might save their lives,” he said.

Smoke Free Sweden is calling on global health authorities to adopt evidence-based policies that distinguish clearly between combustible tobacco – the primary cause of tobacco-related death – and lower-risk nicotine alternatives.

“Public health policy must be grounded in science and real-world outcomes,” Dr Human added. “Sweden’s experience shows that when adult smokers are given legal access to safer nicotine alternatives, smoking rates fall faster than almost anywhere else in the world.”

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