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Tracking the genetic passport of COVID-19

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Implications of different strands of Coronavirus

In late July, scientists claimed that there were six strands of the Coronavirus that caused COVID-19, then there was talk of eight. Sudden outbreaks in the US and Europe have caused speculation that deadlier, infectious strains of the virus may be circulating, with some early studies hinting at as many as 30 kinds of the virus. Coronavirus infections surpassed the 400,000 mark in the first six months alone, exemplifying its formidability as a fast mutating virus. Since the original outbreak in Wuhan, the Coronavirus has infected over 47,428,000 claiming over 1,213,000 lives. Over 11,000 cases have been reported locally with 23 fatalities. Could genetic sequencing better prepare health authorities to deal with the pandemic?

Sequencing could also help to identify which strands are more tenacious and which are dying out. In turn health authorities could use such information to learn how to mitigate the spread of COVID-19, and which medical interventions work best. This is where open-source projects such as NextStrain.org comes in. NextStrain uses genetic sequences of viruses collected from patients, contributed by health authorities from around the world, to track the evolution of epidemics in global maps and phylogenetic charts, the family trees for viruses.

According to Professor Benjamin Howden at the Doherty Institute, Australia, quoted in The Sydney Morning Herald, sequencing or tracking the virus’s ‘genetic passport’, in other words tracing from where a specific strand had been ‘imported’, has now revolutionised how health authorities fight pandemics, and will become critically important in countries that have recently eased out of lockdown. For example, in circumstances where clusters emerge with no clear source, looking for connections in the genetic code of the virus could make contact tracing much more efficient in a country like Sri Lanka where many have been repatriated from countries where COVID-19 is wreaking havoc.

According to health authorities the new strain of the virus, which originated in a new cluster in Minuwangoda, is far more virulent compared to the first wave between March and April. With the virus spreading fast, detected in practically all districts, several hundred patients are reported each day, according to Chief Epidemiologist Dr Sudath Samaraweera.

The latest mutation is unique in its ubiquity, leading to conflagrations in Europe, US and, now Asia. Laboratory experiments suggest that the new strain, officially designated D614G, and familiarly known among scientists as ‘G’, because it has lead to the genetic instruction for the amino acid glycine (G) to be altered, is more infectious and has a higher viral load, making people who have contracted this particular strain more likely to spread it. In fact, the new strain is thought to be as much as 10 times more infectious. The ‘G’ strain, which first appeared in January, is found in the dominant variant of the coronavirus, while the ‘L’ strain that originated in Wuhan is gradually disappearing. The ‘G’ strain, associated with outbreaks in Europe and US, is believed to have originated in Germany, according to NextStrain cofounder Trevor Bedford, a computational biologist at the Fred Hutchinson Cancer Research Center in Seattle, quoted in National Geographic. But nothing is definitive when it comes to the Coronavirus, warns Bedford. Researchers are forced to strike a high-stakes balance between disseminating information quickly and assuring their accuracy.

Scripps Research virologist, Hyeryun Choe, quoted in The Washington Post article titled, ‘This Coronavirus mutation has taken over the world. Scientists are trying to understand why’, points out that, fortunately the ‘G’ strain does not make patients any sicker, despite its higher viral load and any vaccine based on the original strain would be just as effective on the new strain.

Researchers claim that different types or variants of COVID-19 maybe distinguished by a unique set of symptoms. Most pronounced symptoms of COVID-19 include fever, shortness of breath, fatigue, muscle aches, headaches and of course a persistent cough. But several symptoms were later included in diagnostics, as they were increasingly reported by COVID-19 positive patients, such as a loss of sense of taste and smell, the medical terms of which are ageusia and anosmia, respectively. A study by the UK’s King’s College London has grouped these into six ‘symptom clusters’, with a spectrum of breathing difficulties.

1. Flu-like with no fever:

Headache, loss of smell, muscle pains, cough, sore throat, chest pain, no fever.

2. Flu-like with fever:

Headache, loss of smell, cough, sore throat, hoarseness, fever, loss of appetite.

3. Gastrointestinal:

Headache, loss of smell, loss of appetite, diarrhoea, sore throat, chest pain, no cough.

4. Severe level one, fatigue:

Headache, loss of smell, cough, fever, hoarseness, chest pain, fatigue.

5. Severe level two, confusion:

Headache, loss of smell, loss of appetite, cough, fever, hoarseness, sore throat, chest pain, fatigue, confusion, muscle pain.

 

6. Severe level three, abdominal and respiratory: Headache, loss of smell, loss of appetite, cough, fever, hoarseness, sore throat, chest pain, fatigue, confusion, muscle pain, shortness of breath, diarrhoea, abdominal pain.

According to the King’s College research, quoted in the World Economic Forum article titled ‘COVID-19: Could your earliest symptoms predict how ill you’ll get?’, earliest symptoms might help predict how sick someone could become with the progress of the disease. According to the study 16 percent of group 1 patients were admitted to hospital, while almost half of those in group 6 were. Those of groups 4,5 and 6 were older patients with underlying health conditions ranging from diabetes to obesity.

 

As such, Charles Chiu, professor of medicine and infectious disease at the University of California, San Francisco School of Medicine, in USA Today article, ‘8 strains of the coronavirus are circling the globe. Here’s what clues they’re giving scientists’, says that it is unlikely that the different symptoms are related to people being infected with different strains of the virus.

In more positive news, the Coronavirus mutates at a fairly steady rate, approximately 20 mutations per year, according to Professor Francois Balloux, who heads the genetics institute at University College London, quoted in The Sydney Morning Herald. It is not as prolific as influenza, a virus that mutates at such an alarming rate that it requires an updated vaccine every season to keep up with all its mutations. Moreover, research has found that no one strain of the virus is more deadly than another.

Strains are also unlikely to grow more lethal as they evolve. In fact, Australian Government agency, Commonwealth Scientific and Industrial Research Organisation (CSIRO), dangerous pathogens lab, Professor Seshadri Vasan believes that, since a virus’s main objective is to spread and not kill off its hosts, over time the Coronavirus will become milder, the way past pandemic flu strains have, as they adapted to their new host. But it could become a recurring phenomenon, much like influenza, at least until vaccination programmes stamp it out. On the bright side, a virus that mutates comparatively slow is unlikely to change to evade a vaccine, opines scientists. (SP)

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Govt.’s choice is dialogue over confrontation

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By Jehan Perera

Preparing for the forthcoming UN Human Rights Council cannot be easy for a government elected on a nationalist platform that was very critical of international intervention. When the government declared its intention to withdraw from Sri Lanka’s co-sponsorship of the October 2015 resolution No. 30/1 last February, it may have been hoping that this would be the end of the matter. However, this is not to be. The UN Human Rights High Commissioner’s report that will be taken up at the forthcoming UNHRC session in March contains a slate of proposals that are severely punitive in nature and will need to be mitigated. These include targeted economic sanctions, travel bans and even the involvement of the International Criminal Court.

Since UN Secretary General Ban Ki-Moon’s visit in May 2009 just a few days after the three-decade long war came to its bloody termination, Sri Lanka has been a regular part of the UNHRC’s formal discussion and sometimes even taking the centre stage. Three resolutions were passed on Sri Lanka under acrimonious circumstances, with Sri Lanka winning the very first one, but losing the next two. As the country became internationally known for its opposition to revisiting the past, sanctions and hostile propaganda against it began to mount. It was only after the then Sri Lankan government in 2015 agreed to co-sponsor a fresh resolution did the clouds begin to dispel.

Clearly in preparation for the forthcoming UNHRC session in Geneva in March, the government has finally delivered on a promise it made a year ago at the same venue. In February 2020 Foreign Minister Dinesh Gunawardena sought to prepare the ground for Sri Lanka’s withdrawal from co-sponsorship of UN Human Rights Council resolution No 30/1 of 2015. His speech in Geneva highlighted two important issues. The first, and most important to Sri Lanka’s future, was that the government did not wish to break its relationships with the UN system and its mechanisms. He said, “Sri Lanka will continue to remain engaged with, and seek as required, the assistance of the UN and its agencies including the regular human rights mandates/bodies and mechanisms in capacity building and technical assistance, in keeping with domestic priorities and policies.”

Second, the Foreign Minister concluding his speech at the UNHRC session in Geneva saying “No one has the well-being of the multi-ethnic, multi-lingual, multi-religious and multi-cultural people of Sri Lanka closer to their heart, than the Government of Sri Lanka. It is this motivation that guides our commitment and resolve to move towards comprehensive reconciliation and an era of stable peace and prosperity for our people.” On that occasion the government pledged to set up a commission of inquiry to inquire into the findings of previous commissions of inquiry. The government’s action of appointing a sitting Supreme Court judge as the chairperson of a three-member presidential commission of inquiry into the findings and recommendations of earlier commissions and official bodies can be seen as the start point of its response to the UNHRC.

 

 

NEGATIVE RESPONSE

 

The government’s setting up of a Commission of Inquiry has yet to find a positive response from the international and national human rights community and may not find it at all. The national legal commentator Kishali Pinto Jayawardene has written that “the tasks encompassed within its mandate have already been performed by the Lessons Learnt and Reconciliation Commission (LLRC, 2011) under the term of this President’s brother, himself the country’s Executive President at the time, Mahinda Rajapaksa.” Amnesty International has stated that “Sri Lanka has a litany of such failed COIs that Amnesty International has extensively documented.” It goes on to quote from the UN High Commissioner for Human Rights that “Domestic processes have consistently failed to deliver accountability in the past and I am not convinced the appointment of yet another Commission of Inquiry will advance this agenda. As a result, victims remain denied justice and Sri Lankans from all communities have no guarantee that past patterns of human rights violations will not recur.”

It appears that the government intends its appointment of the COI to meet the demand for accountability in regard to past human rights violations. Its mandate includes to “Find out whether preceding Commissions of Inquiry and Committees which have been appointed to investigate into human rights violations, have revealed any human rights violations, serious violations of the international humanitarian law and other such serious offences.” In the past the government has not been prepared to accept that such violations took place in a way that is deserving of so much of international scrutiny. Time and again the point has been made in Sri Lanka that there are no clean wars fought anywhere in the world.

International organisations that stands for the principles of international human rights will necessarily be acting according to their mandates. These include seeking the intervention of international judicial mechanisms or seeking to promote hybrid international and national joint mechanisms within countries in which the legal structures have not been successful in ensuring justice. The latter was on the cards in regard to Resolution 30/1 from which the government withdrew its co-sponsorship. The previous government leaders who agreed to this resolution had to publicly deny any such intention in view of overwhelming political and public opposition to such a hybrid mechanism. The present government has made it clear that it will not accept international or hybrid mechanisms.

 

 

SEQUENTIAL IMPLEMENATION

 

In the preamble to the establishment of the COI the government has made some very constructive statements that open up the space for dialogue on issues of accountability, human rights and reconciliation. It states that “the policy of the Government of Sri Lanka is to continue to work with the United Nations and its Agencies to achieve accountability and human resource development for achieving sustainable peace and reconciliation, even though Sri Lanka withdrew from the co-sponsorship of the aforesaid resolutions” and further goes on to say that “the Government of Sri Lanka is committed to ensure that, other issues remain to be resolved through democratic and legal processes and to make institutional reforms where necessary to ensure justice and reconciliation.”

As the representative of a sovereign state, the government cannot be compelled to either accept international mechanisms or to prosecute those it does not wish to prosecute. At the same time its willingness to discuss the issues of accountability, justice and reconciliation as outlined in the preamble can be considered positively. The concept of transitional justice on which Resolution No 30/1 was built consists of the four pillars of truth, accountability, reparations and institutional reform. There is international debate on whether these four pillars should be implemented simultaneously or whether it is acceptable that they be implemented sequentially depending on the country context.

The government has already commenced the reparations process by establishing the Office for Reparations and to allocate a monthly sum of Rs 6000 to all those who have obtained Certificates of Absence (of their relatives) from the Office of Missing Persons. This process of compensation can be speeded up, widened and improved. It is also reported that the government is willing to consider the plight of suspected members of the LTTE who have been in detention without trial, and in some cases without even being indicted, for more than 10 years. The sooner action is taken the better. The government can also seek the assistance of the international community, and India in particular, to develop the war affected parts of the country on the lines of the Marshall Plan that the United States utilized to rebuild war destroyed parts of Europe. Member countries of the UNHRC need to be convinced that the government’s actions will take forward the national reconciliation process to vote to close the chapter on UNHRC resolution 30/1 in March 2021.

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Album to celebrate 30 years

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Rajiv Sebastian had mega plans to celebrate 30 years, in showbiz, and the plans included concerts, both local and foreign. But, with the pandemic, the singer had to put everything on hold.

However, in order to remember this great occasion, the singer has done an album, made up of 12 songs, featuring several well known artistes, including Sunil of the Gypsies.

All the songs have been composed, very specially for this album.

Among the highlights will be a duet, featuring Rajiv and the Derena DreamStar winner, Andrea Fallen.

Andrea, I’m told, will also be featured, doing a solo spot, on the album.

Rajiv and his band The Clan handle the Friday night scene at The Cinnamon Grand Breeze Bar, from 07.30 pm, onwards.

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LET’S DO IT … in the new normal

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The local showbiz scene is certainly brightening up – of course, in the ‘new normal’ format (and we hope so!)

Going back to the old format would be disastrous, especially as the country is experiencing a surge in Covid-19 cases, and the Western Province is said to be high on the list of new cases.

But…life has to go on, and with the necessary precautions taken, we can certainly enjoy what the ‘new normal’ has to offer us…by way of entertainment.

Bassist Benjy, who leads the band Aquarius, is happy that is hard work is finally bringing the band the desired results – where work is concerned.

Although new to the entertainment scene, Aquarius had lots of good things coming their way, but the pandemic ruined it all – not only for Aquarius but also for everyone connected with showbiz.

However, there are positive signs, on the horizon, and Benjy indicated to us that he is enthusiastically looking forward to making it a happening scene – wherever they perform.

And, this Friday night (January 29th), Aquarius will be doing their thing at The Show By O, Mount Lavinia – a beach front venue.

Benjy says he is planning out something extra special for this particular night.

“This is our very first outing, as a band, at The Show By O, so we want to make it memorable for all those who turn up this Friday.”

The legendary bassist, who lights up the stage, whenever he booms into action, is looking forward to seeing music lovers, and all those who missed out on being entertained for quite a while, at the Mount Lavinia venue, this Friday.

“I assure you, it will be a night to be remembered.”

Benjy and Aquarius will also be doing their thing, every Saturday evening, at the Darley rd. Pub & Restaurant, Colombo 10.

In fact, they were featured at this particular venue, late last year, but the second wave of Covid-19 ended their gigs.

Also new to the scene – very new, I would say – is Ishini and her band, The Branch.

Of course, Ishini is a singer of repute, having performed with Mirage, but as Ishini and The Branch, they are brand new!

Nevertheless, they were featured at certain five-star venues, during the past few weeks…of their existence.

 

 

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