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An era ends

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In Memoriam: Sirisena Cooray

by Tisaranee Gunasekara

“Where has the tree gone, that locked Earth to the sky?”

Philip Larkin (Going)

Sirisena Cooray gave his final interview three months before his death. A Sunday Sinhala paper had carried a wildly inaccurate account of the Premadasa era. Sirisena Cooray called the editor and asked for an opportunity to set the record straight. The resulting interview ran to two full pages and was carried on consecutive Sundays.

Sirisena Cooray spent the last years of his life as an observer of the Lankan political scene. He was willing to talk to those who sought his advice, but shunned further involvement. Though distressed by the national trajectory, he opted for silence, unable to identify with any of the political players. But these self-imposed restraints vanished when Ranasinghe Premadasa was maligned. Sirisena Cooray could withstand extreme personal and political vicissitudes. Any attack on the memory of his leader and friend was another matter.

“An obituary is a perfect framing devise,” wrote New Yorker columnist Susan Orleans. It is also a balance-sheet of a life. Sirisena Cooray’s story was inextricably intertwined with the story of independent Ceylon/Sri Lanka and the story of Ranasinghe Premadasa. The Premadasa-Cooray relationship defined and shaped not just Sirisena Cooray’s life but also that of Ranasinghe Premadasa and thereby modern Lankan history.

Without Sirisena Cooray, there would have been a Minister Premadasa, perhaps even a Prime Minister Premadasa, but never a President Premadasa.

20th Century was the age of Causes. No time in history was played on a grander canvas, or a bloodier one. It was on this stage of seemingly infinite possibilities that Ranasinghe Premadasa and Sirisena Cooray would live their lives. The national and international ferment did enable a breadth of vision and a reach that was not available to preceding generations. Premadasa could organise lectures for the young members of the Sucharitha movement on Politics (including an overview of Karl Marx and of different political and governance systems) and Religions and Doctrines (a summary of the four main world religions). Young Sirisena and his friends could meet and invite leaders of major political parties to attend a ceremony organised by their newly formed Sucharitha branch. Change was in the air, and dreaming big was normal. Two young men from Colombo Central could imagine one of them becoming the leader of the country electorally, peacefully transforming the land to the benefit of their marginalised brethren.

Busy years; happy years

Sirisena Cooray became a UNPer because of his father, a founder member of the party. But supporting Ranasinghe Premadasa was his own choice, though one backed by both his parents. Starting with a small part in Premadasa’s 1956 Ruwanwella campaign, Cooray’s involvement grew until in 1960 he took over Premadasa’s successful parliamentary bid from Colombo Central.

Though helping Premadasa became an axiomatic part of his life, Cooray never intended to become a politician. He enjoyed his work as a cinema manager. He particularly relished being sent to theatres across the country, the constant moving perfectly in synch with his own restless nature, and his desire to see and experience new places. He would recall with unconcealed glee that over a period of 13 years he managed 12 cinemas, involving 12 relocations with his patient wife and growing family in tow.

For many years, the two strands of his life, the personal and the political, moved side by side. This changed in the 1970s, when at the urging of Premadasa and the UNP, he contested and won the Suduwella ward and entered the Colombo Municipal Council. The transition was cemented once JR Jayewardene took over the UNP, and Ranasinghe Premadasa became his de facto second in command. Sirisena Cooray found himself in the thick of the UNP’s political campaigns, criss-crossing the country, at Premadasa’s side, while also building the Colombo Central organisation into a formidable electoral machine.

1977 was a year of radical break, both good and bad. Its most progressive component was the fracture with familial and dynastic politics. “I have no princes or princesses to crown,” was a constant refrain of JR Jayawardene’s campaign. His remade UNP consisted mostly of new men who were not sons, brothers or nephews of other politicians. Perhaps none symbolised this break with the past more than Ranasinghe Premadasa, an outsider both in class and caste terms. Colombo Central was Premadasa’s political family, the home of his growing tribe. And Sirisena Cooray was the man in charge of that vital space.

Throughout his life, Sirisena Cooray would be beset by two warring impulses. He loved travel, loved new experiences and vistas. He also wanted to be at Premadasa’s side, to help him realise their shared vision. After 1977, he planned to try his hand at farming, sold his house in Colombo and brought a land in Katana in readiness. Premadasa persuaded him to become the head of the Common Amenities Board, and set in motion plans to improve the living conditions of Colombo’s poor. In 1978, he became Sri Lanka’s high commissioner in Malaysia. One year into the job, he was summoned home by President Jayewardene, and asked to contest the Colombo Mayoralty. “Cooray, this man (Premadasa) can’t do without you,” JRJ told him.

His 10 years as mayor were a fruitful time, a period in his life he would recall with nostalgia. The work of these years included the construction of the new public library, setting up a network of mobile libraries serving Colombo’s poorer areas, the construction of the Khettarama Stadium solely with CMC funds, expertise, and labour and improving and expanding sanitation facilities by replacing bucket lavatories with water sealed closets.

“There were 5,000 bucket lavatories in just Colombo North,” Cooray recalled in President Premadasa and I: Our story. “Every morning, these buckets had to be removed manually. The refuse was taken in open lorries and the whole area used to stink. It was an appalling sight. I had found out all these details during my stint at the Common Amenities Board. Our plan was to provide residents with the necessary assistance and get them to construct septic tanks. This programme worked and as a result today there are no bucket lavatories in Colombo.”

The significance of this achievement becomes clear when one considers that Burj Khalifa, the tallest building in the world, is not connected to a municipal sewage system. Its waste (and those of many other Dubai skyscrapers) is trucked out of the city to a treatment facility, where the trucks wait in queue up to 24 hours. Glitzy infrastructure can exist side by side with the absence of basic facilities when leaders prioritise appearance over substance.

His failure to prevent Black July was one of Sirisena Cooray’s lasting regrets. But it was due to his and Premadasa’s approach to housing that prevented Colombo Central, the most multi-ethnic and multi-religious electorate in Sri Lanka, from going up in flames. In the new apartment blocks, flats were allocated in such a manner that each floor consisted of families of different ethnicities and religions. You could not set fire to your neighbour’s house without endangering your own.

Presidency and beyond

From 1978 to 1988, Ranasinghe Premadasa and Sirisena Cooray were engaged in the slow political and organisational build up towards a future Premadasa presidency. When the UNP was compelled to make Premadasa the candidate, Cooray naturally became the campaign manager (a term first used by the late Roshan Pieris). The campaign took off with the famous Me Kawda, Monawada Karanne (Who is this? What is he doing?) poster campaign. The slogan was coined by a journalist friend of Victor Hettigoda who attended the first preparatory meeting. The overnight campaign was the work of the Colombo Central organisation, the one Cooray had nursed over the years.

The campaign hit a snag soon after when the Kandy UNP organisation and security forces agreed that holding the inaugural rally in the hill capital was impossible due to security considerations. Ranasinghe Premadasa, uncharacteristically, toyed with the idea of a postponement. Cooray refused, saying, “Sir, in that case resign from the candidacy, because postponing the first meeting is like accepting defeat.” Instead he took over the task of organising the meeting from the Kandy party apparatus and handed it over to Colombo Central branch. The meeting was held as planned.

Once the presidency was won, Cooray wanted to continue as mayor. But Premadasa wanted him in parliament and he eventually gave in, as he always would. Premadasa needed a custodian for his housing programme and his Colombo Central electorate. Cooray was the ideal choice, both in terms of ability and experience. Even more important was the issue of loyalty. There was no one Premadasa trusted more.

Absolute loyalty was not uncritical loyalty. Cooray had differences of opinion, and didn’t hesitate to express them to Premadasa. For instance, he felt that the premiership should have been given to either Lalith Athulathmudali or Gamini Dissanayake, and argued unsuccessfully with Premadasa on the issue. But whenever need arose, he was there, be it the impeachment, raising of the Maligawila Buddha statue or building a model village in Bodgaya at a time when relations between Colombo and Delhi were as cold as the Himalayas.

Post-assassination, had Cooray dumped the Premadasa legacy, had he changed colours to suit the new environment, he could have continued with his political career. But for him such betrayal was as impossible as not breathing. Cooray could say no to the offer of premiership without regrets. But he could not stop defending Premadasa.

Ranasinghe Premadasa who built so much never named a single village or a byroad after himself. It was Sirisena Cooray who named the Khettarama stadium after him, post-assassination. (Cooray who also built much never named even a passageway after himself. Like a majority of political leaders of that time, they built to serve, not to perpetuate their name at public expense). Premadasa’s subsequent rehabilitation in public memory and political arena was the result of the work Cooray enabled and presided over. Without Cooray, Premadasa’s memory would have become lost in fogs of lies and misrepresentations.

After he (and the UNP) lost the July 1960, election, Premadasa called a meeting at Lawrence College to thank his supporters. Looking at the audience, he turned to Cooray and said, “Sirisena, never forget the poor people of Colombo Central.” When Premadasa won the presidency, Cooray reminded him of this promise at a pubic function in the mayoral residence. That promise they made to each other was the other reason Cooray continued with his memorial and social service work, after he lost Premadasa.

In the last one year, with his public involvement severely limited by pandemic related health restrictions, Cooray still found a way to continue with his work. He would help individuals who visited or called him seeking assistance. If help was impossible, he would still listen to them, insisting that to the poor and the powerless, even a sympathetic ear meant much. For the Premadasa tribe, Sirisena Cooray was the last remaining link with an imagined, desired, and only partially-realised world where life was not determined by birth or bank balance. Until his death, he tried to be true to that role history and choice has bestowed on him.



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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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