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More on leopards, two beautiful plains and camping in the wild

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by Walter R. Gooneratne

(continued from last week)

As this would be our last day, we decided to trek to two fabulous places as described by Babun. There were two large plains called Waraketiya and Dananayake Eliya. They were about six miles from camp towards Muduntalawa. The track was again riddled with fresh pug marks of leopard, but no animals were seen. As it was still drizzling, they were probably taking cover in the jungle.

After about two hours of walking, we came to Waraketiya Eliya (eliya =plain). It was a large plain about 200 yards wide and bounded by two streams, Kumbukpitia Ara on the west and Suandandan Ara on the east. While walking through the swampy plain we surprised a herd of wild buffaloes wallowing in a mud hole. Fortunately, they bolted in panic on seeing us. Except for a few peafowl, no animals were seen in the plain. The two streams coalesced to form the Dharage Ara. We followed this stream for some distance and came upon Dananayake plain, which was much larger than Waraketiya Eliya.

An elephant was browsing on the branches of a tree. We watched it for a little while and then made a detour downwind. We then went on to explore the vast plain. In a water-hole, a large sounder of wild boar, accompanied by numerous sucklings was feeding on the yams of lotus, so dear to them. Wild boar flesh was what we wanted to take back home, and here was our chance. They ignored us and continued to feed, while Babun and Pervey were debating on which was the fattest. Having made his choice, Pervey fired on a big fat boar with his rifle. At the shot, the whole sounder took flight, including the targeted animal.

I thought he had missed it and was about to fire again, when he collapsed and died a short distance away. We now regretted our decision not to bring the jeep as we would now have to carry the heavy burden ourselves, The pig was cut into two and each half slung on a pole. Pervey and Babun took one half, and Mackie and I the other. As young doctors, our funds were limited; hence the sparing use of the jeep.

As we were returning, a short distance from Waraketiya, some monkeys were calling to our right. Babun said they were calling on account of a leopard, and wanted me to come with him. Glad to be relieved of my burden even for a short while, I dropped the carcass and followed him. A huge bear was ambling towards us. I fired at him with the rifle and unfortunately hit him in the middle of his spine.. His hind limbs were paralysed and he came crawling on his forelimbs, yelling blue murder. My rifle had two triggers. The rear one had to be squeezed first to activate the front or hair trigger. In my excitement I had squeezed the front trigger and the bullet ploughed harmlessly into the ground. My magazine was now empty. Fortunately, Pervey came running up and gave the wounded animal the coup-de-grace. It was a huge male bear.

As it would be impossible to carry both carcasses, to my immediate relief it was decided to go back to camp, refresh ourselves with a bath and lunch, and bring the jeep to take the prizes home. We hoped no marauding leopard would deprive us of our pork before we came back. When we arrived in camp, the cook was missing, and the food had not been cooked, We were worried if any mishap had befallen him. When we called him, he sheepishly answered from the top of a nearby tree. He himself did not know how he was able to shin up the tree, as he had much difficulty in coming down even with our help. He explained what had happened.

Shortly after we left, he had set about preparing our midday meal with his back to the track. Suddenly there was a blood curdling sound from behind. At first he had thought it was a devil bird, but on turning round he saw the devil himself in the form of a bear screaming obscenities (as described by him) and tearing away into the jungle in the opposite direction. The next thing he knew was that he found himself up the tree. What had happened was that the bear had come ambling down the track and accidentally trod on the embers of the previous night’s camp-fire.

After lunch we took the jeep and brought back the carcasses, which fortunately were untouched.

Our last evening was spent with Babun skinning the bear and Mackie taking a rest. Pervey and I walked to Thalakola Wewa, but saw nothing to interest us. The next day we bade farewell to our new-found friend, Babun and returned to Kandy about 10 that night. The first person to greet us the next morning was old Seetin Singho. He, like Shylock, had come for his pound of kara mus, which he received with much glee.

In those days, there was a visitor’s book kept at the park office at Yala, where those who entered its precincts wrote their comments. My entry in the visitor’s book about this trip was displayed about a couple of years ago in the museum at the Park office. Later it was replaced by the entries of a similar trip by the Hon. D.S.Senanayake and his party, which if I remember right, included the late Mr. Sam Elapata. On inquiry from the park officials, I was informed that they were unable to trace my entry.

Leopard at Kumana

For quite sometime I had been contemplating visiting Kumana as I had heard so much about its famed bird sanctuary, enormous herds of deer and other attractions. My usual companions, Pervey Lawrence and Mackie Ratwatte were not free to join me when the opportunity came quite unexpectedly when my friend, the late Dr. Ivor Obeysekera suggested that we make a trip to Kumana. Of course I jumped at it.

The party consisted of Ivor, his wife, my wife Nirmalene and myself. At 3.30 am on April 12, 1956 we left Kandy in an old Willys jeep and a trailer that Ivor had borrowed from a friend. We had obtained permits from the Department of Wildlife (as it was then called) to shoot peafowl, jungle fowl, deer and leopard. Ivor had not used a gun before and did not own one. I had with me my usual armoury of weapons, namely a 7.9 mm Mauser, a Webley, Scott double-barrel shot gun and .22 calibre Hornet.

Bellowing crocodiles

In those days there was very little traffic, specially at that hour, and the roads were well maintained. After a pleasant drive we arrived in Batticaloa about 8 am for breakfast at my brother’s home. After a sumptuous meal we left for Pottuvil and Kumana on the coastal road. The next stop was just past Komari in the shade of a huge mara tree for a packeted lunch provided by my brother. About ten yards from where we were, was a culvert, and suddenly there came a loud booming sound from its direction. We were at a loss to realize what it could be. I had not heard anything like this before. I picked up my rifle and walked cautiously to investigate. I was stunned by what I saw. There, lying in the shallow water was a medium-sized crocodile bellowing away. As it was half submerged, bubbles of air billowed out of the sides of its mouth. I beckoned to the others to come up, but as soon as they peeped over, the creature saw us and crept into the culvert.

This is the first time I had heard this sound. I heard this call once more when going down the Mahaweli in the company of Mr. Thilo Hoffman and a few others. At one point we found a nest of baby crocodiles, probably a day or two old. One of our party picked up a few of them in his folded shirt. Their squealing alerted the mother who came charging through the water from nearby. He dropped the hatchlings and bolted for dear life. The mother then came up to the nest and sent out her bellowing call warning all and sundry to keep away from her family. We did not waste much time on the way and traveled through Pottuvil and Panama. At Halawa we saw an elephant feeding some distance from the road and left him undisturbed.

Old warriors

We arrived at Okanda without further incident and met the ranger, Peter Jayawardene for the first time. This was the beginning of a lifelong friendship with a most colourful character. The legendry Garuwa was to be our guide and tracker. He had as his assistant Wasthuwa, an equally experienced jungle man. As it was getting late, Garuwa decided that we camp for the night at Itikala Kalapuwa. At that time of the evening, the surface of the kalapuwa or lagoon glistened like a sheet of molten silver. Putting up camp was a simple affair. A rope was tied between two trees and a tarpaulin slung over it and the four corners tethered to convenient trees. Four camp beds completed the five-star comfort.

All the day’s fatigue and grime were washed away in the cool water of the nearby kema or rock water-hole. After a stiff sundowner, we were treated to a delicious dinner of rice, pol sambol, which is a mixture of mainly chilli powder and coconut scrapings, homemade ambulthial, which is a traditional fish curry and dhal or lentil curry prepared by the wives, ably assisted by Wasthuwa.

Bait for the leopard

As Garuwa was keen that we shoot an animal as bait for leopard, as well as for the pot, we left camp at about 6 am. He suggested that we walk, since the jeep would disturb the animals. The wives insisted on accompanying us. We walked till about 7.30 and the sun was getting uncomfortably hot, but we had not seen any worthwhile animal except a lone elephant in the distance. I suggested that we go back to camp, have breakfast and go for a drive by jeep. However, Garuwa said that there was a good water-hole fairly close by and it may be worth checking.

A good 10 minutes’ walk brought us to a circular muddy pond about 40 yards in diameter. Peeping through the foliage, we saw a large sambhur stag wallowing in the mud. It died immediately it was shot, and as we had to bring the jeep and trailer to take back the carcass, I volunteered to walk back with Wasthuwa and bring these.

When we came back, Garuwa suggested that we go back to the village and pick up a young lad who could cook, thus relieving the ladies from that chore. This turned out to be a real blessing. He was a young man of about 20 years, and not only was he an excellent cook but also a very willing and efficient worker. We nicknamed him Kadisara, meaning quick-acting.

After breakfast, the carcass was divided in two. The head and the upper part of the thorax, which were to be the leopard bait, were tied to the jeep and dragged to the site where it was to be secured. A prowling leopard had a better chance of spotting the drag mark and finding the kill. The site for the bait was at a point about 20 yards down the track leading to the Kumana tank, on the edge of the forest. This area was open country, but about 30 yards further down, the road ended in high forest.

It was earlier decided to move camp to the regular site on the banks of Kumbukkan Oya, but as it was too sunny, we decided to postpone the operation for the cool of the evening. As it was now about 11 am, Garuwa suggested that we catch some crabs to add variety to our lunch. He cut a stake about three feet long and sharpened it to a point at one end. He then took us to Itikala Kalapuwa. Having alighted from the vehicle, he asked me to come with him to the water of the lagoon, which was only about a foot deep near the edge. Peering into the water, he showed me a crab and spiked it with the stake. Seven crabs were thus captured.

Having come back to the camp, we had a bath in the kema and rounded off with a glass of ice-cold beer. In no time Kadisara prepared a delicious lunch with venison and crab curry. As there was no murunga in the jungle, he picked up some leaves from the kara plant, if I remember right, to flavour the crab curry. A well earned siesta was taken before the evening’s chores.

Camp was soon dismantled, the jeep and trailer were loaded and we were on our way to the new camp site, which we reached at about 5 pm. What a beautiful spot it was. There was a wide expanse of river before us with its banks lined with lofty kumbuk trees, which spread their canopy over us like a giant umbrella.

(Excerpted from Jungle Journeys in Sri Lanka Experiences and encounters Edited by CG Uragoda)



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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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