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The Sandahiru event – celebrating failure

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by Anura Gunasekera

A few days ago President Gotabaya Rajapaksa(GR), the first military man and, unarguably, the most ignorant in the ways of governance to occupy the presidential seat, celebrated the completion of two years as the eighth president of the Republic of Sri Lanka. The salutation coincided with the formal vesting with the Sangha, of the “Sandahiru Seya” in Anuradhapura, a project commenced during brother Mahinda’s last term as president. A towering stupa rising above the Jetawana and the Abhayagiri, ostensibly to honour the services rendered by the armed forces and the police in our ethnic conflict but, in reality, a monument to the Rajapaksa delusions of grandeur, aligns the Rajapaksa Family dynasty with the Sinhala Kings. A tribute to the heroic is justified but the supreme incongruity of conflating the quintessential Buddhist symbol, with success in a bloody military campaign, is inconsequential to a hegemonic mindset. The incompatibility was also ignored by the Rajapaksa-adoring Sangha, including the Anunayake Theros of both Asgiriya and Malwatte Chapters, who participated and enthusiastically endorsed its purpose.

Notwithstanding a grandiose commemoration, as Rajapaksa’s second year in the presidency ends and the year 2021 draws to a close, the country stands mired in calamities on every public front.

The Crisis

The economy is in disaster mode. Foreign reserves which were at USD 7.5 Billion in November 2019, when GR took office, had declined to USD 2.8 Billion by August 2021. Despite Central Bank Governor Cabraal’s blithe assurance that the economy can be restructured without IMF assistance, and that wildly reckless money-printing has no impact on inflation, banks are unable to provide importers with forex to import essentials, whilst prices of basic commodities are placing them beyond the reach of ordinary consumers. According to most economists, in the real world, when money printing increases in a background of stagnant or declining national output, all other factors being equal, hyper-inflation is the certain outcome. Recent historical examples are too numerous to quote here. However, Cabraal, who is one of the architects and, also, a highly privileged inhabitant of the Rajapaksa Dystopia, is obviously reading from a different text!

For the last few months, in every village, town and city across the island, for the first time since the Sirimavo Bandaranaike regime 50 years ago, desperate citizens have been waiting in queues to buy the most basic items. There are frequent shortages of sugar, rice, milk powder and cooking fuel; very recently, suppliers ran short of kerosene oil, the only convenient and affordable alternative to cooking gas. Gathering firewood is not an option, especially for the four million urban population of Sri Lanka.

The government has responded to the foreign exchange shortage by imposing drastic regulations to limit dollar usage, declaring over 600 imported items, including mobile phones, clothing, household appliances and a range of foods, as non-essential. Vehicles imports are also included in the restrictions.

Prices of essential foods, vegetables and staples have seen an astronomic escalation during 2021, due to low supply, either because of import restrictions or, in the case of locally grown items, a result of poor harvests due to denial- through unavailability- of basic nutrient inputs, and disruptions in the supply chain from distant growing areas.

The Cause

The pandemic has contributed to the crisis, dismantling livelihoods with some of the monthly paid subjected to wage cuts or layoffs, whilst daily paid workers are denied earnings through inability to access places of work or, because the lockdown has compelled the closure of many small establishments, which rely mainly on casual labour. As in many countries in the developing world, in Sri Lanka, the informal, small and medium scale entrepreneurial sector collectively supports more livelihoods, than either the State or the corporate sector. However, the Covid pandemic is only a contributory factor to an escalating socio-economic disaster. The government, through the implementation of a series of imprudent and ill-conceived policies, has aggravated the situation to a degree beyond retrieval.

Immediately after assuming the presidency, GR ordered sweeping tax concessions, which resulted in the diminution of government revenues by about 30% in 2020. These concessions were beneficial to a minute proportion of the population, which actually needed no such relief. They did not cascade to the ordinary citizen. Soon thereafter, to bridge the cash supply deficit the money printing spree commenced, according to some sources injecting as much as an additional 35% – 40% in to the economy, by mid-2021.

The pandemic Task Force was led by a retired army commander, appointed by a president unable to distinguish between the scientific complexities of fighting a virus, and the tactical requirements of assaulting an enemy garrison. This mindset was also compounded by an inherent insensitivity to the suffering of ordinary people. The mismanagement of the project in its early, critical stages led to an escalation of infections and deaths, especially amongst the elderly who were denied vaccinations at the outset. Successive waves of infection even led to embarrassing State sponsorship of miracle cures- the ridiculous “Dhammika Elixir” and the casting of holy water pots in to flowing water!!

Whilst people were desperately scrabbling around to sustain themselves in a setting of loss of income, essential item scarcities and other privations, overnight, the president decreed a ban on the use of inorganic fertilizer and agro-chemicals. All professional agriculturists in the country (the writer was one for over 50 years) and scientists in related disciplines, have pointed out the certainty of the disastrous outcomes from the implementation of this irrational, unscientific and impractical policy; the adverse consequences are already visible in the case of short term crops, especially rice and vegetables, whilst the impact on the long-term plantation crops, particularly tea, will very soon be evident in the form of crop declines, diminished exports and shrinking foreign exchange earnings.

The Response

The island-wide uprising of despairing farmers, beating and burning effigies of senior ministers and demanding a reversal of the fertilizer ban, was met with the promise of organic fertilizer as an alternative. The imported organic nutrient, apparently a mixture of sea weed and faeces- a second virus from China after Corona- was found unsuitable, leading to imports from India of “liquid nitrogen”, a product untried on a large scale in that country. One of the President’s responses to the anguish of the farmers was to declare at a public meeting that he could, if he considered it desirable, use the army to seize the farming community by the scruff of its collective neck and compel them to use organic fertilizer!!

The ban on the slaughter of cattle is a similarly ill-considered directive. Alleviating animal suffering is a noble cause but the consequences of the ban will be dire for several hundred thousand people. The cattle rearing industry is multi-faceted and interconnected. Milk production, beef supply and the supply of animal skin to the tanning industry go hand-in-hand. Dairy industry, which is essentially a small farmer collective enterprise, becomes unviable unless unproductive animals are converted to meat. This ban will disempower around 200,000 individual farmers island-wide, many of them Muslims in the Eastern province. The certain consequences will be the decline of local milk production, scarcity of allied dairy products and the unpreventable escalation of illicit cattle slaughter. That proverb of unknown origin, that ” The Road to Hell is Paved With Good Intentions,” is an apt commentary on both the fertilizer and cattle slaughter ban.

Younger brother Basil, hailed by Rajapaksa acolytes as an economic genius of Einsteinian proportions- despite the absence of previous experience and known academic background – has produced a budget reinforced by bloated statistics and unrealizable dreams. His disgracefully incoherent Budget speech, delivered in Sinhala, justifiably lampooned in multiple forums, was not improved by his rambling, garbled contributions in a subsequent English language interview on the same subject, with Ms Indeewari Amuwatte on Ada Derana. The questions were intelligent, precise and designed to elicit clarity. The responses were vague, evasive and inarticulate, by a man struggling to defend the indefensible in a medium clearly unfamiliar to him; at best a cringe-worthy performance.

Consequences

A frustrated electorate propelled GR in to power in justifiable disgust at the dysfunctional governance of the Sirisena- Wickramesinghe regime, only to be confronted, in less than two years, with an ineptitude of colossal proportions. The enormous parliamentary advantage of a two-thirds majority and a presidency with unlimited power, the two moving in parallel rather than in unison, has paved the way for an economic and social disaster. It is an inevitable consequence of the 20th Amendment, which has expanded the powers of the President, whilst encroaching on the authority of the parliament and the judiciary. When the individual so elected believes that he is the sole repository of wisdom in governance – despite a total lack of experience in the field and a wretched absence of ordinary commonsense – chaos ensues. That is what we see everyday, in mass protests against moronic directives.

The only visible success in governance in Sri Lanka today is the inexorable onward march of the Rajapaksa project, which commenced during Mahinda Rajapaksa’s first term and, after a slight hiccup during the abortive Sirisena regime, has gathered a terrifying new momentum since end 2019. It is conservatively estimated that about 64% of the country’s economy is directly controlled by the Rajapaksa family and those connected to it. In a country rapidly sliding in to an abyss where lies the bleak certainty of food and other essential item scarcities – including pharmaceuticals – widespread malnutrition, loss of employment and livelihoods, declining foreign exchange earnings, disruption to education at all levels and the disintegration of the society, the only glow in a leaden sky comes from the Rajapaksa comet. The State will surely fail but the First Family will surely prosper.

Unless a disoriented and vacillatory opposition quickly gathers its wits, firstly jettisoning the toxic Ranil Wickremesinghe and then rallying round Premadasa – not necessarily the best of men but the only possible alternative – the Rajapaksa dynastic succession, from elder brother to younger brother and from uncle to nephew, and thereafter to another sibling or relative, is a certainty.

Gotabaya Rajapaksa was elected President by the convergence of normally divergent political forces. But, once elected, by-passing the legislature and other democratic institutions, he has chosen to govern through the armed forces and a collection of “Task Forces”, staffed or led by ex-military men, and other disciples and profiteers, answerable to only him. A spineless, collusive and essentially corrupt legislature has become a rubber stamp to his will. A reading of the two year performance report establishes beyond doubt that the “Viyathmaga” is the road to certain ruin, and that the “Eliyamaga” will condemn this country to economic darkness before the Gotabaya presidency ends.

Very recently, parliamentarian Kumara Welgama delivered a speech at the Diyawanna assembly, amusing, but brutally frank, in its exposure of the venality of recent regimes and the familial considerations which overrode national interests in decision making at the highest levels of governance, whilst highlighting the aberrant mentality that pervades the current dispensation. It was also prophetic in the warnings sounded to the ruling regime. Not one of his statements were contested. It must now be clear to all that when madmen are allowed to run the asylum, lunacy becomes institutionalized and insanity infiltrates governance.



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Features

A Good Guide to the Omicron Variant

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By M.C.M. Iqbal, PhD

Despite the WHO adopting a neutral system to name the variants of the coronavirus that keep emerging (using letters of the Greek alphabet), the Omicron variant is associated with South Africa. The last variant of the virus to emerge was the Delta variant, which surfaced in December 2020, in India. There are two more letters between Delta and Omicron in the Greek alphabet that the WHO decided not to use. These are ‘Nu’ and ‘Xie’, which the WHO thought could be confused with ‘new’ while Xie is a common surname in China.

The Omicron variant is spreading in many countries. With the number of infected persons rising and another wave expected, many countries in Europe have imposed the usual methods to arrest the spread, with immediate lockdowns. However, scientists are still collecting data to find out how bad Omicron is, since the data seems to indicate that in South Africa, the disease is not as bad as the Delta variant. At the same time, in Europe, there is no significant change in the number of persons hospitalized. Of immediate concern to health authorities are, is the Omicron variant spreading faster than the earlier variants, does it cause more or less severe disease, and can it bypass the vaccines available?

Discovery

Scientists in South Africa announced on 25 November the discovery of a new variant of the coronavirus. On 26 November, the WHO named it Omicron. Although South Africa has been labeled as the country of origin, the virus was identified in neighbouring Botswana. In addition, there are reports of an earlier detection of this variant in the Netherlands.

PCR tests look for four markers on the virus genome to identify it as the coronavirus. The tests in Botswana showed a reduced sensitivity because one of the four targets was not being detected. These samples were sent to South Africa, where scientists have state-of-the-art facilities to look for changes in the genome of the virus. Changes are found by reading the ‘letters’ of the virus genome (called sequencing) and comparing it to the already available genome of the virus. The new Omicron variant had many more changes than the Delta variant.

Global status

By 14th January, the Omicron variant had spread to 116 countries in all six continents since its discovery on 26 November 2021. The figure below shows the gradual replacement of the presently dominant Delta variant by the Omicron variant; at present global data on the coronavirus, maintained by Nextstrain (https:// nextstrain.org/ncov/open/global) shows a decline of the Delta variant from 88% on 30th October 2021 to 42% on 8th January 2022, while correspondingly the Omicron variant has increased from less than 1% to 56%. Nextstrain is a global database presenting a real-time view of the evolution of the genomes of the coronavirus and other globally important pathogens. The interactive platform provides information to professionals and the public to understand the spread and evolution of pathogens, including information on individual countries.

Distribution of Delta and Omicron variants on 1st January 2022 from Nextstrain. (Please see graph)

What’s unique about Omicron?

Unlike the previous variants of the coronavirus, this variant has over 30 changes (mutations) to its spike (a protein), the characteristic flower-like protrusion on its surface. It was these changes to the spike, one of the four targets of the PCR test that raised alarm bells in Botswana. This spike makes the coronavirus special – it is the key it uses to gain entry into the cells in our throat and lungs. The previous variants, Alpha and Delta also had changes in their spike protein, enabling them to enter cells more efficiently and thus making them more infectious. The vaccines against the virus are based on this spike, and the antibodies produced by our immune system are specific to the spike protein. Thus, any significant changes to the spike means the previous vaccines may not be effective against the newly changed spikes on the Omicron variant.

While the Omicron variant can spread rapidly, it appears to cause milder disease compared to the Alpha and Delta variants. Scientists believe this is because Omicron infects the upper airways or the throat, and not the lungs further down. Based on experiments done on hamsters and mice, scientists found the concentration of the virus was much lower in the lungs than in their throat. The earlier variants of the coronavirus caused severe damage to the lungs of the infected people, with extreme cases needing oxygen. This does not seem to be the case with Omicron. Scientists believe the changes to the spike enables the virus to enter cells in the throat more easily than in the lungs.

It can spread rapidly

The virus is quickly expelled into the air if it infects and multiplies in the throat. Since it causes a milder form of the disease, infected persons may be unaware that they carry the virus. They would be moving about socially and at work, spreading the virus. Thus, the obvious means of slowing or preventing the spread of the virus is to strictly wear the mask at all times, and avoid social gatherings.

Studies have suggested that the period between exposure to the virus and onset of symptoms has also reduced to three days for Omicron. At the pandemic’s beginning, this was more than five days, and for the Delta variant it was four days.

What is of immediate concern?

Of concern to scientists is the better ability of the Omicron to spread rapidly in the population and its suspected ability to bypass our immune system. Our immune system is our internal defense system, using antibodies and an arsenal of chemicals and cells. The available vaccines are designed on the coronavirus variants circulating in the population. Thus, major changes to the coronavirus can reduce the efficiency of the available vaccines. Both these concerns have been observed in the past month: Omicron can spread more rapidly than the presently dominant Delta variant, and observations on vaccinated people show a reduced ability by the vaccines to prevent infections, compared to the Delta variant. This has called for booster doses for people who have already received the two mandatory doses. In Israel, even a fourth vaccination is being administered.

How could the variant have evolved?

Variants of the coronavirus result from changes to the virus’s genome, called mutations. What is troubling about the Omicron variant is that it has many mutations in its spike. Mutations happen spontaneously as the virus multiplies in our bodies and spreads to others. Thus, the virus gradually accumulates small changes to its advantage. These advantages are infecting us more efficiently, spreading to others more easily, and multiplying more rapidly. Scientists believe that one possibility is that the virus circulated in a small isolated group of people (say a village), piling up the mutations over time, and then escaping into a broader population, and then eventually crossing borders.

Another possibility is that it developed in a single individual and spread to others. This happens when a person has low immunity, resulting in a prolonged infection because the immune system cannot eliminate the virus. This leads to the virus developing changes (mutating) to overcome the mild immune response. Answering this question needs scientists to painstakingly reconstruct the history of the virus, using tools from molecular biology. Unfortunately, locating patient zero is difficult since it is impossible to analyze the virus (or sequence its genome) of all the persons infected with the Omicron variant. What is usually possible is to determine a general area or community and the time of origin.

What can we do about it?

Vaccinate! This is the primary tool we have to prevent the spread of the virus and not give it opportunities to multiply. In addition, we should rigorously follow the simple rules we are familiar with – wear the mask when outside, physically distance ourselves, and follow hygienic practices by washing our hands with soap, and avoiding touching our nose and face with possibly contaminated hands.

The good news

The coronavirus has been with us for over two years. Many were infected and have recovered from the virus during this period, providing natural immunity. Others have acquired immunity through vaccinations. When a new variant infects these people, they will manifest a milder form of the disease. This may explain the reduced hospitalisation of Omicron patients.

A booster dose to those already vaccinated or were naturally infected by the coronavirus, appears to provide reasonable protection against the Omicron variant.

And the bad news

The Omicron variant can evade immunity from previous infections. A recent analysis of surveillance data from South Africa, involving over two million persons, indicated suspected reinfections of those previously infected. This is in contrast to Beta and Delta variants, which did not lead to reinfections on such a scale.

The Future

The coronavirus is here for the long haul. Variants will keep emerging, and it seems unlikely it can be eradicated. The media should help counter vaccine hesitancy and the spread of misinformation. As individuals, we need to understand the biology of the virus to avoid spreading the virus and infecting ourselves and others. Science has to be supported in a broad sense to develop strategies by the health authorities and policymakers.

Further reading

S. Wild. How the Omicron variant got so many scary mutations. Scientific American, 3rd December 2021.

Michael Chan Chi-wai.

G. Vogel and K. Kupferschmidt. Early lab studies hint Omicron may be milder. But most scientists reserve judgment. Science, 20th December 2021.

K. Kupferschmidt and G. Vogel. Omicron threats remain fuzzy as cases explode. Science, 7 January 2022.

(The writer is a scientist in Plant and Environmental Sciences, National Institute of Fundamental Studies, Hanthane Road, Kandy. He can be reached at iqbal.mo@nifs.ac.lk)

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Rebirth in Buddhism

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By Dr. Justice Chandradasa Nanayakkara

The question of what happens after death naturally arises in the mind of thoughtful people, as we do not know what lies beyond death, because no one has ever returned to the living to recount his experiences life after death. Almost every religion across the world has a defined belief on what happens when a person dies, yet the question is still widely debated and discussed without any finality being reached on the issue. Most of the religious teachers from the earliest times, have been unanimous in affirming that life continues beyond the grave, but they differ widely on the question of what form and in what manner the survival takes place. Nevertheless, mankind continues to believe in some form of survival after death.

Regarding the question of survival after death, thinkers have generally followed one of two philosophical concepts. That is to say annihilationism and eternalism (in Buddhist, ucchedavada and sassatavada). First view is held by nihilists who claim that there is no life after death. They hold the view with the disintegration of the physical body the personality ceases to exist. This view accords with materialistic philosophy, which refuses to accept knowledge of mental conditionality. Those who hold the second view think that there is an abiding entity which exists forever and individual personality persists after death in a recognizable form as an entity called soul, spirit or self. This belief in some form or another is the basis of all theistic religions.

If you stick to the first view and deny that there is no continuity of life after death there would not be no moral law and vipaka (actions and results) operating in the universe enunciated by Lord Buddha and there would be no object in practicing self-restraint or endeavoring to free ourselves of the craving thanha which brings suffering in its wake. The cardinal teachings of the Buddha such as path to nibbana, Four Noble Truths and the eightfold path would be rendered nugatory and meaningless if death is followed by complete extinction. Similarly, those who believe eternalism which presupposes that individual personality persists after death in the form of soul or self as an enduring personality by means of transmigration is also rejected by Buddhism. This view runs counter to the very essence of Buddhism which denies existence of soul. This is the teaching of anatta doctrine, which distinguishes buddhism from other religions and marks it out from all other religious concepts.

In view of the virtual impossibility of establishing the truth of survival after death through empirical methods, question arises what is the attitude of science to this important and abstruse question which has baffled the minds of many people. Although, it is not possible to posit ‘rebirth’ as a scientific fact many men of science are of the opinion that mental, moral and physical inequalities can be accounted for on no other hypothesis than ‘rebirth’ hypothesis.

The idea of a cycle of birth and ‘rebirth’ is part of the teachings of the Lord Buddha. For many Buddhists death is not seen as an end, but rather as a continuation. Buddhists believe a person goes from life to life and see it another part of their long journey through samsara.

Buddhists do not regard ‘rebirth’ as a mere theory but as fact verifiable by evidence and it forms a fundamental tenet in Buddhism along with the concept of karma. Therefore, two principles-kamma and ‘rebirth’ are fundamental to understanding the teachings of Buddha. Kamma and ‘rebirth’ go in arm in arm. According to Buddhism there is no life after death or life before birth independent of kamma. Kamma is an immutable law of cause and effect, and we cannot avoid its consequences. Where there is kamma there must be ‘rebirth’. Most experiences in our present life are the results of our previous actions. Our actions of body, speech and mind (volitional activities) rebound back to us either in the present life or in some future life. It is the karma that conditions ‘rebirth’, past kamma conditions the present birth, the present kamma in combination with past kamma conditions the future. The present is the offspring of the past, and becomes in turn the parent of the future. For Buddhist death is not complete annihilation of a being though that particular life span ended, the force which hitherto actuated it is not destroyed. After death the life flux of man continues ad infinitum as long as there is ignorance and craving. Man will be able to put an end his repeated series of births by realizing nibbana, the complete annihilation of all forms of craving (Narada Thera).

The Buddhist doctrine of ‘rebirth’ should be differentiated from the theory of reincarnation, which implies transmigration of a soul and its invariable ‘rebirth’, as it is enunciated in Hinduism.

In his book What the Buddha Taught, Walpola Rahula Thera posed the question “if we can understand that in this life we can continue without a permanent, unchanging substance like self or soul, why can’t we understand that those forces themselves can continue without a self or soul behind them after the non-functioning of the body? ‘When this physical body is no more capable of functioning, energies do not die with it, but continue to take some other shape or form, which we call another life… physical and mental energies which constitute the so called being have within themselves the power to take a new form, and grow gradually and gather force to the full: King Milinda questioning venerable Nagasena asked: “Venerable Nagasena, does ‘rebirth’ take place without anything transmigrating? Yes, O king, ‘rebirth’ takes place without anything transmigrating? “Give me illustration, venerable Sir. Suppose, O king, a man were to light a light from light pray, would the one light have passed over to the other light?” “Nay, indeed, Venerable Sir. “In exactly the same way, O king, does ‘rebirth’ take place without anything transmigrating.

In this connection, it should be mentioned the word ‘rebirth’ is not a satisfactory one, as it implies that there is something that after death takes on flesh again. It connotes transmigration of soul or other entity consequent to a death of a person. The Pali Word used in buddhism is arising or Phunabba.

As there is no soul or self in Buddhism, question arises if there is no soul or self what is there to be reborn. This has been most vexed question among many religious scholars. This has been a topic of debate for centuries. According to buddhism there is no enduring, substantial or independently existing entity that transmigrates from life to life instead there is simply an apparent continuity of momentary consciousness from one life time to the next that is imbued with impressions or traces (samskaras)of the actions one has committed in the past. For Buddhists everything is changing and nothing is permanent. So, when a person dies not he but his energies that shape him take a new form. New life is connected to previous life through kamma. There is rapid succession of thoughts throughout the life continuum.

The Buddha is our greatest authority on ‘rebirth. Therefore, for Buddhist no other evidence is necessary is prove ‘rebirth’.

On the very night of His enlightenment during the first watch, enlightenment, Buddhas mind travelled back through all of his unaccountable past lives. This was facilitated by the development of retro cognitive knowledge. Though his mind stretched back to countless eons he never saw a beginning to his past existence. He found no beginning and no end. He also saw all the beings in the universe being born, living dying and being reborn over and over again without end, all trapped in a web spun by their past actions. This process is the round of ‘rebirth’ known as samsara, which means wandering from life to life with no particular direction or purpose.

The Buddha before his enlightenment as bodhisattva was born in different forms of existence. As such Buddhist have a firm belief in many realms of existence, both above and below the human realm. Therefore, we can safely assume we all have lived through countless different lifetimes before being born in the world and our birth here as a human being is the result of predominantly good kamma we have committed in the past life. Those good kamma may have been done in many life times before, or more likely done in the previous life. Therefore, the quality of future births depends on the moral quality of our actions now.

In Dhammachackka Sutta too in his first discourse referring to second noble truth, Buddha declared this very craving is that leads to ‘rebirth’.

In ancient Greece philosophers like Empedocles and Pythagoras too taught the doctrine of ‘rebirth’ and Plato made it an important assumption in his philosophy, as pointed out by Ven Piyadassi Thera.

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A Good Guide to the Omicron Variant

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By M.C.M. Iqbal, PhD

Despite the WHO adopting a neutral system to name the variants of the coronavirus that keep emerging (using letters of the Greek alphabet), the Omicron variant is associated with South Africa. The last variant of the virus to emerge was the Delta variant, which surfaced in December 2020, in India. There are two more letters between Delta and Omicron in the Greek alphabet that the WHO decided not to use. These are ‘Nu’ and ‘Xie’, which the WHO thought could be confused with ‘new’ while Xie is a common surname in China.

The Omicron variant is spreading in many countries. With the number of infected persons rising and another wave expected, many countries in Europe have imposed the usual methods to arrest the spread, with immediate lockdowns. However, scientists are still collecting data to find out how bad Omicron is, since the data seems to indicate that in South Africa, the disease is not as bad as the Delta variant. At the same time, in Europe, there is no significant change in the number of persons hospitalized. Of immediate concern to health authorities are, is the Omicron variant spreading faster than the earlier variants, does it cause more or less severe disease, and can it bypass the vaccines available?

Discovery

Scientists in South Africa announced on 25 November the discovery of a new variant of the coronavirus. On 26 November, the WHO named it Omicron. Although South Africa has been labeled as the country of origin, the virus was identified in neighbouring Botswana. In addition, there are reports of an earlier detection of this variant in the Netherlands.

PCR tests look for four markers on the virus genome to identify it as the coronavirus. The tests in Botswana showed a reduced sensitivity because one of the four targets was not being detected. These samples were sent to South Africa, where scientists have state-of-the-art facilities to look for changes in the genome of the virus. Changes are found by reading the ‘letters’ of the virus genome (called sequencing) and comparing it to the already available genome of the virus. The new Omicron variant had many more changes than the Delta variant.

Global status

By 14th January, the Omicron variant had spread to 116 countries in all six continents since its discovery on 26 November 2021. The figure below shows the gradual replacement of the presently dominant Delta variant by the Omicron variant; at present global data on the coronavirus, maintained by Nextstrain (https:// nextstrain.org/ncov/open/global) shows a decline of the Delta variant from 88% on 30th October 2021 to 42% on 8th January 2022, while correspondingly the Omicron variant has increased from less than 1% to 56%. Nextstrain is a global database presenting a real-time view of the evolution of the genomes of the coronavirus and other globally important pathogens. The interactive platform provides information to professionals and the public to understand the spread and evolution of pathogens, including information on individual countries.

Distribution of Delta and Omicron variants on 1st January 2022 from Nextstrain. (Please see graph)

What’s unique about Omicron?

Unlike the previous variants of the coronavirus, this variant has over 30 changes (mutations) to its spike (a protein), the characteristic flower-like protrusion on its surface. It was these changes to the spike, one of the four targets of the PCR test that raised alarm bells in Botswana. This spike makes the coronavirus special – it is the key it uses to gain entry into the cells in our throat and lungs. The previous variants, Alpha and Delta also had changes in their spike protein, enabling them to enter cells more efficiently and thus making them more infectious. The vaccines against the virus are based on this spike, and the antibodies produced by our immune system are specific to the spike protein. Thus, any significant changes to the spike means the previous vaccines may not be effective against the newly changed spikes on the Omicron variant.

While the Omicron variant can spread rapidly, it appears to cause milder disease compared to the Alpha and Delta variants. Scientists believe this is because Omicron infects the upper airways or the throat, and not the lungs further down. Based on experiments done on hamsters and mice, scientists found the concentration of the virus was much lower in the lungs than in their throat. The earlier variants of the coronavirus caused severe damage to the lungs of the infected people, with extreme cases needing oxygen. This does not seem to be the case with Omicron. Scientists believe the changes to the spike enables the virus to enter cells in the throat more easily than in the lungs.

It can spread rapidly

The virus is quickly expelled into the air if it infects and multiplies in the throat. Since it causes a milder form of the disease, infected persons may be unaware that they carry the virus. They would be moving about socially and at work, spreading the virus. Thus, the obvious means of slowing or preventing the spread of the virus is to strictly wear the mask at all times, and avoid social gatherings.

Studies have suggested that the period between exposure to the virus and onset of symptoms has also reduced to three days for Omicron. At the pandemic’s beginning, this was more than five days, and for the Delta variant it was four days.

What is of immediate concern?

Of concern to scientists is the better ability of the Omicron to spread rapidly in the population and its suspected ability to bypass our immune system. Our immune system is our internal defense system, using antibodies and an arsenal of chemicals and cells. The available vaccines are designed on the coronavirus variants circulating in the population. Thus, major changes to the coronavirus can reduce the efficiency of the available vaccines. Both these concerns have been observed in the past month: Omicron can spread more rapidly than the presently dominant Delta variant, and observations on vaccinated people show a reduced ability by the vaccines to prevent infections, compared to the Delta variant. This has called for booster doses for people who have already received the two mandatory doses. In Israel, even a fourth vaccination is being administered.

How could the variant have evolved?

Variants of the coronavirus result from changes to the virus’s genome, called mutations. What is troubling about the Omicron variant is that it has many mutations in its spike. Mutations happen spontaneously as the virus multiplies in our bodies and spreads to others. Thus, the virus gradually accumulates small changes to its advantage. These advantages are infecting us more efficiently, spreading to others more easily, and multiplying more rapidly. Scientists believe that one possibility is that the virus circulated in a small isolated group of people (say a village), piling up the mutations over time, and then escaping into a broader population, and then eventually crossing borders.

Another possibility is that it developed in a single individual and spread to others. This happens when a person has low immunity, resulting in a prolonged infection because the immune system cannot eliminate the virus. This leads to the virus developing changes (mutating) to overcome the mild immune response. Answering this question needs scientists to painstakingly reconstruct the history of the virus, using tools from molecular biology. Unfortunately, locating patient zero is difficult since it is impossible to analyze the virus (or sequence its genome) of all the persons infected with the Omicron variant. What is usually possible is to determine a general area or community and the time of origin.

What can we do about it?

Vaccinate! This is the primary tool we have to prevent the spread of the virus and not give it opportunities to multiply. In addition, we should rigorously follow the simple rules we are familiar with – wear the mask when outside, physically distance ourselves, and follow hygienic practices by washing our hands with soap, and avoiding touching our nose and face with possibly contaminated hands.

The good news

The coronavirus has been with us for over two years. Many were infected and have recovered from the virus during this period, providing natural immunity. Others have acquired immunity through vaccinations. When a new variant infects these people, they will manifest a milder form of the disease. This may explain the reduced hospitalisation of Omicron patients.

A booster dose to those already vaccinated or were naturally infected by the coronavirus, appears to provide reasonable protection against the Omicron variant.

And the bad news

The Omicron variant can evade immunity from previous infections. A recent analysis of surveillance data from South Africa, involving over two million persons, indicated suspected reinfections of those previously infected. This is in contrast to Beta and Delta variants, which did not lead to reinfections on such a scale.

The Future

The coronavirus is here for the long haul. Variants will keep emerging, and it seems unlikely it can be eradicated. The media should help counter vaccine hesitancy and the spread of misinformation. As individuals, we need to understand the biology of the virus to avoid spreading the virus and infecting ourselves and others. Science has to be supported in a broad sense to develop strategies by the health authorities and policymakers.

Further reading

S. Wild. How the Omicron variant got so many scary mutations. Scientific American, 3rd December 2021.

Michael Chan Chi-wai.

G. Vogel and K. Kupferschmidt. Early lab studies hint Omicron may be milder. But most scientists reserve judgment. Science, 20th December 2021.

K. Kupferschmidt and G. Vogel. Omicron threats remain fuzzy as cases explode. Science, 7 January 2022.

(The writer is a scientist in Plant and Environmental Sciences, National Institute of Fundamental Studies, Hanthane Road, Kandy. He can be reached at iqbal.mo@nifs.ac.lk)

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