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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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Features

Glimmers of hope?

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The newly appointed Cabinet Ministers leaves Cass un-uplifted. She need not elaborate. She wishes fervently that Dr Harsha de Silva will leave party loyalty aside and consider the country. Usually, it’s asking politicians to cast aside self-interest, which very rarely is done in the political culture that came to be after the 1970s. Thus, it is very unusual, completely out of the ordinary to appeal to Dr Harsha to forego party loyalty and do the very needful for the country by accepting the still vacant post of Minister of Finance. We are very sorry Eran W too has kept himself away.

Some of Cassandra’s readers may ask whether she is out of her right mind to see glimmers of hope for the country. She assures them she is as sane as can be; she does cling onto these straws like the dying man does. How else exist? How else get through these dire times?

What are the straws she clings to? News items in The Island of Tuesday 24 May.

‘Sirisena leaves Paget Road mansion in accordance with SC interim injunction.’ And who was instrumental in righting this wrong? The CPA and its Executive Director Dr Pakiasothy Saravanamuttu. It is hoped that revisions to the system will come in such as giving luxury housing and other extravagant perks to ex-presidents and their widows. Sri Lanka has always lived far beyond its means in the golden handshakes to its ex- prezs and also perks given its MPs. At least luxury vehicles should not be given them. Pensions after five years in Parliament should be scrapped forthwith.

‘Letter of demand sent to IGP seeking legal action against DIG Nilantha Jayawardena.’ Here the mover is The Centre for Society and Religion and it is with regard to the Easter Sunday massacre which could have been prevented if DIG Jayawardena as Head of State Intelligence had taken necessary action once intelligence messages warned of attack on churches.

‘CIABOC to indict Johnston, Keheliya and Rohitha’. It is fervently hoped that this will not be another charge that blows away with the wind. They do not have their strongest supporter – Mahinda R to save them. We so fervently hope the two in power now will let things happened justly, according to the law of the land.

‘Foreign Secy Admiral Colombage replaced’. And by whom? A career diplomat who has every right and qualification for the post; namely Aruni Wijewardane. If this indicates a fading of the prominence given to retired armed forces personnel in public life and administration, it is an excellent sign. Admiral Colombage had tendered his resignation, noted Wednesday’s newspaper.

‘Crisis caused by decades of misuse public resources, corruption, kleptocracy – TISL’.

Everyone knew this, even the despicable thieves and kleptocrats. The glaring question is why no concerted effort was made to stop the thieving from a country drawn to bankruptcy by politicians and admin officers. There are many answers to that question. It was groups, mostly of the middle class who came out first in candle lit vigils and then at the Gotagogama Village. The aragalaya has to go down in history as the savior of our nation from a curse worse than war. The civil war was won against many odds. But trying to defeat deceit power-hunger and thieving was near impossible. These protestors stuck their necks out and managed to rid from power most of the Rajapaksa family. That was achievement enough.

Heartfelt hope of the many

The newly appointed Cabinet Ministers leaves Cass un-uplifted. She need not elaborate. She wishes fervently that Dr Harsha de Silva will leave party loyalty aside and consider the country. Usually, it’s asking politicians to cast aside self interest, which very rarely is done in the political culture that came to be after the 1970s. Thus, it is very unusual, completely out of the ordinary to appeal to Dr Harsha to forego party loyalty and do the very needful for the country by accepting the still vacant post of Minister of Finance. We are very sorry Eran W too has kept himself away. As Shamindra Ferdinando writes in the newspaper mentioned, “Well informed sources said that Premier Wickremesinghe was still making efforts to win over some more Opposition members. Sources speculated that vital finance portfolio remained vacant as the government still believed (hoped Cass says) Dr Harsha de Silva could somehow be convinced to accept that portfolio.”

Still utterly hopeless

Gas is still unavailable for people like Cass who cannot stand in queues, first to get a token and then a cylinder. Will life never return to no queues for bare essentials? A woman friend was in a petrol queue for a solid twelve hours – from 4 am to 4 pm. This is just one of million people all over the country in queues. Even a common pressure pill was not available in 20 mg per.

Cassandra considers a hope. We saw hundreds of Sri Lankans all across the globe peacefully protesting for departure of thieves from the government. The ex-PM, Mahinda Rajapaksa’s answer to this was to unleash absolute terror on all of the island. It seems to be that with Johnson a younger MP stood commandingly.

Returning from that horror thought to the protesters overseas, Cass wondered if each of them contributed one hundred dollars to their mother country, it would go a long way to soften the blows we are battered with. Of course, the absolute imperative is that of the money, not a cent goes into personal pockets. The donors must be assured it goes to safety. Is that still not possible: assuring that donations are used for the purpose they are sent for: to alleviate the situation of Sri Lankans? I suppose the memory of tsunami funds going into the Helping Hambantota Fund is still fresh in memory. So much for our beloved country.

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Ban on agrochemicals and fertilisers: Post-scenario analysis

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By Prof. Rohan Rajapakse

(Emeritus Professor of Agriculture Biology UNIVERSITY OF RUHUNA and Former Executive Director Sri Lanka Council of Agriculture Research Policy)

There are two aspects of the ban on agrochemicals. The first is the ban on chemical fertilisers, and the second is the ban on the use of pesticides. Several eminent scientists, Dr Parakrama Waidyanatha (formerly the Soil Scientist of RRI), Prof OA Ileperuma (Former Professor of Chemistry University of Peradeniya), Prof C. S. Weeraratne (former Professor of Agronomy University of Ruhuna), Prof D. M. de Costa University of Peradeniya, Prof. Buddhi Marambe (Professor in Weed Science University of Peradeniya) have effectively dealt with the repercussion of the ban on chemical fertilisers which appeared in The Island newspaper on recently.

The major points summarised by these authors are listed below.

FERTILISER ISSUE

1. These scientists, including the author, are of the view that the President’s decision to totally shift to organic agriculture from conventional could lead to widespread hunger and starvation in future, which has become a reality. Organic farming is a small phenomenon in global agriculture, comprising a mere 1.5% of total farmlands, of which 66% are pasture.

2. Conventional farming (CF) is blamed for environmental pollution; however, in organic farming, heavy metal pollution and the release of carbon dioxide and methane, two greenhouse gases from farmyard manure, are serious pollution issues with organic farming that have been identified.

3. On the other hand, the greatest benefit of organic fertilisers as against chemical fertilisers is the improvement of soil’s physical, chemical and biological properties by the former, which is important for sustained crop productivity. The best option is to use appropriate combinations of organic and chemical fertilisers, which can also provide exacting nutrient demands of crops and still is the best option!

4. Sri Lanka has achieved self-sufficiency in rice due to the efforts of the Research Officers of the Department of Agriculture, and all these efforts will be in vain if we abruptly ban the import of fertiliser. These varieties are bred primarily on their fertiliser response. While compost has some positive effects such as improving soil texture and providing some micronutrients, it cannot be used as a substitute for fertiliser needed by high yielding varieties of rice. Applying organic fertilisers alone will not help replenish the nutrients absorbed by a crop. Organic fertilisers have relatively small amounts of the nutrients that plants need. For example, compost has only 2% nitrogen (N), whereas urea has 46% N. Banning the import of inorganic fertilisers will be disastrous, as not applying adequate amounts of nutrients will cause yields to drop, making it essential to increase food imports. Sri Lankan farmers at present are at the mercy of five organizations, namely the Central Department of Agriculture, the Provincial Ministry of Agriculture, the Private sector Pesticide Companies, the Non-Government organizations and the leading farmers who are advising them. Instead, improved agricultural extension services to promote alternative non-chemical methods of pest control and especially the use of Integrated Pest Management.

Locally, pest control depends mostly on the use of synthetic pesticides; ready to use products that can be easily procured from local vendors are applied when and where required Abuse and misapplication of pesticides is a common phenomenon in Sri Lanka. Even though many farmers are aware of the detrimental aspects of pesticides they often use them due to economic gains

We will look at the post scenario of
what has happened

1. The importation of Chemical fertilisers and Pesticides was banned at the beginning of Maha season 1 on the advice of several organic manure (OM) promoters by the Ministry of agriculture.

2. The Ministry of Agriculture encouraged the farmers to use organic manure, and an island-wide programme of producing Organic manure were initiated. IT took some time for the government to realize that Sri Lanka does not have the capacity to produce such a massive amount of OM, running into 10 tons per hectare for 500000 hectares ear marked in ma ha season.

3. Hence the government approved the importation of OM from abroad, and a Company in China was given an initial contract to produce OM produced from Seaweed. However, the scientists from University of Peradeniya detected harmful microorganisms in this initial consignment, and the ship was forced to leave Sri Lankan waters at a cost of US dollar 6.7 million without unloading its poisonous cargo. No substitute fertiliser consignment was available.

4. A committee in the Ministry hastily recommended to import NANO RAJA an artificial compound from India to increase the yield by spraying on to leaves. Sri Lanka lost Rs 863 million as farmers threw all these Nano Raja bottles and can as it attracts dogs and wild boar.

Since there is no other option the Ministry promised to pay Rs 50000 per hectare for all the farmers who lost their livelihood. It is not known how much the country lost due to this illogical decision of banning fertilisers and pesticides.

Recommendations

1. Judicious use of pesticides is recommended.

2. The promotion and the use of integrated pest management techniques whenever possible

3. To minimize the usage of pesticides:

Pesticide traders would be permitted to sell pesticides only through specially trained Technical Assistants.

Issuing pesticides to the farmers for which they have to produce some kind of a written recommendation by a local authority.

Introduction of new mechanism to dispose or recycle empty pesticide and weedicide bottles in collaboration with the Environment Ministry.

Laboratory-testing of imported pesticides by the Registrar of Pesticides at the entry-point to ensure that banned chemicals were not brought into the country.

Implementation of trained core of people who can apply pesticides.

Education campaigns to train farmers, retailers, distributors, and public with the adverse effects of pesticides.

Maximum Residue Level (MRL) to reduce the consumer’s risk of exposure to unsafe levels.

Integrated pest Management and organic agriculture to be promoted.

1. To ensure the proper usage of agrochemicals by farmers

All those who advised the Minister of Agriculture and the President to shift to OM still wield authority in national food production effort. The genuine scientists who predicted the outcome are still harassed sacked from positions they held in MA and were labelled as private sector goons. The danger lies if the farmers decide not to cultivate in this Maha season due to non-availability of fertilisers and pesticides the result will be an imminent famine.

The country also should have a professional body like the Planning Commission of

India, with high calibre professionals in the Universities and the Departments and

There should be institutions and experts to advise the government on national policy matters.

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Thomians triumph in Sydney 

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Nothing is happening for us, at this end, other than queues, queues, and more queues! There’s very little to shout about were the sports and entertainment scenes are concerned. However, Down Under, the going seems good.

Sri Lankans, especially in Melbourne, Australia, have quite a lot of happenings to check out, and they all seem to be having a jolly good time!

Trevine Rodrigo,

who puts pen to paper to keep Sri Lankans informed of the events in Melbourne, was in Sydney, to taken in the scene at the Sri Lanka Schools Sevens Touch Rugby competition. And, this is Trevine’s report:

The weather Gods and S.Thomas aligned, in Sydney, to provide the unexpected at the Sri Lanka Schools Sevens Touch Rugby competition, graced by an appreciative crowd.

Inclement weather was forecast for the day, and a well drilled Dharmaraja College was expected to go back-to-back at this now emerging competition in Sydney’s Sri Lanka expatriate sporting calendar.

But the unforeseen was delivered, with sunny conditions throughout, and the Thomians provided the upset of the competition when they stunned the favourites, Dharmaraja, in the final, to grab the Peninsula Motor Group Trophy.

Still in its infancy, the Sevens Touch Competition, drawn on the lines of Rugby League rules, found new flair and more enthusiasm among its growing number of fans, through the injection of players from around Australia, opposed to the initial tournament which was restricted to mainly Sydneysiders.

A carnival like atmosphere prevailed throughout the day’s competition.

Ten teams pitted themselves in a round robin system, in two groups, and the top four sides then progressed to the semi-finals, on a knock out basis, to find the winner.

A food stall gave fans the opportunity to keep themselves fed and hydrated while the teams provided the thrills of a highly competitive and skilled tournament.

The rugby dished out was fiercely contested, with teams such as Trinity, Royal and St. Peter’s very much in the fray but failing to qualify after narrow losses on a day of unpredictability.

Issipathana and Wesley were the other semi-finalists with the Pathanians grabbing third place in the play-off before the final.

The final was a tense encounter between last year’s finalists Dharmaraja College and S.Thomas. Form suggested that the Rajans were on track for successive wins in as many attempts.  But the Thomians had other ideas.

The fluent Rajans, with deft handling skills and evasive running, looked the goods, but found the Thomian defence impregnable.  Things were tied until the final minutes when the Thomians sealed the result with an intercept try and hung on to claim the unthinkable.

It was perhaps the price for complacency on the Rajans part that cost them the game and a lesson that it is never over until the final whistle.

Peninsula Motor Group, headed by successful businessman Dilip Kumar, was the main sponsor of the event, providing playing gear to all the teams, and prize money to the winners and runners-up.

The plan for the future is to make this event more attractive and better structured, according to the organisers, headed by Deeptha Perera, whose vision was behind the success of this episode.

In a bid to increase interest, an over 40’s tournament, preceded the main event, and it was as interesting as the younger version.

Ceylon Touch Rugby, a mixed team from Melbourne, won the over 40 competition, beating Royal College in the final.

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