Features
Some oddities of coronavirus mutations
All RNA viruses tend to evolve rapidly; about a million times faster than human genes. Yet for all that, if SARS-CoV-2 stands out at all among them, it is simply because of the markedly slow pace at which it evolves, compared to many of its relatives. For example, it is thought to evolve about five times less rapidly than the biologically related influenza viruses. It has been postulated by Nextstrain, an open-source project that tracks the evolution of pathogens in real time, and other sources as well, that SARS-CoV-2 is accumulating an average of about two mutations per month.
By Dr B. J. C. Perera
MBBS(Cey), DCH(Cey), DCH(Eng), MD(Paed), MRCP(UK), FRCP(Edin), FRCP(Lon), FRCPCH(UK), FSLCPaed, FCCP, Hony FRCPCH(UK), Hony. FCGP(SL)
Specialist Consultant Paediatrician
There is a lot of talk as well as considerable uncertainty and apprehension associated with the spectacle of natural and spontaneous changes or ‘mutations’, as they are called, in the SARS-CoV-2 virus that causes COVID-19. These trepidations are currently apparent, not only among people but also in the medical circles as well. We have all read several accounts of patients who recovered from Covid-19 only to be infected with SARS-CoV-2 again later, allegedly by a different “strain” of the virus. In late August 2020, came news about the world’s first “documented” or “confirmed” case of reinfection with SARS-CoV-2: a man from Hong Kong, diagnosed in March, had contracted “a new virus variant” circulating in Western Europe during the summer. The very next day, news broke out that two people in Europe also appeared to have been reinfected. After that, it was a story about the first American case of the kind, involving a patient in Nevada, who was said to have suffered worse symptoms the second time around. The preprint study which had not been peer-reviewed, on which those reports were based, seems to no longer be available in the global scientific literature.
Yet, for all that, all this talk about newly mutated, perhaps even more virulent forms of SARS-CoV-2, is most definitely igniting and sparking fear and sowing confusion. The vital question is whether there could be either an increase, or for that matter even a decrease, in the severity of the illness caused by these mutant viruses.
For one thing, it is important to keep in mind that isolated cases of reinfection also happen with other viruses. That fact should not necessarily be alarming. Reinfection usually tells us something only about how the human immune system works. On just the face of it, that occurrence is not definitive evidence that a virus does always change in ways that make it more dangerous. Of course, it is well-known that viruses routinely mutate. However, perhaps more importantly, quite a lot of these changes and modifications to their basic structure are bad for the virus itself or even fatal to the virus, according to some scientific studies. Only a minority of mutations are neutral, and only just a tiny minority of mutations are beneficial to the virus itself. The word “mutation” may sound ominous, but it is a rather boring and well-recognised fact of viral life and its implications may not always be all that malevolent for humans.
Yes, of course, the SARS-CoV-2 is mutating, too. One might justifiably ask “So what?”. The million-dollar question is whether it has become more virulent or more infectious than it was when it was first detected in Wuhan in December 2019? The current evidence suggests that it has not been proven to be more virulent. So what indeed?
Like the viruses that give us influenza or measles, SARS-CoV-2 has a genetic code made up of ribonucleic acid (RNA). But RNA is highly mutable, and since SARS-CoV-2 infects us by using our body’s cells to replicate itself again and again, every time its genome is copied, there is a real chance that an error might creep in. That is the unavoidable basic progress of the life-cycle of the virus. Most mutations actually get lost rather quickly, either by chance, or because they damage some part of the main structure or the functions of the virus. Only a small proportion end up spreading widely or lasting for long periods of time. Mutation may be the fuel of evolution but, especially for an RNA virus, it also is just business as usual. Mutations may not always make the virus comply with the celebrated theory of Charles Darwin of survival of the fittest.
All RNA viruses tend to evolve rapidly; about a million times faster than human genes. Yet for all that, if SARS-CoV-2 stands out at all among them, it is simply because of the markedly slow pace at which it evolves, compared to many of its relatives. For example, it is thought to evolve about five times less rapidly than the biologically related influenza viruses. It has been postulated by Nextstrain, an open-source project that tracks the evolution of pathogens in real time, and other sources as well, that SARS-CoV-2 is accumulating an average of about two mutations per month.
When translated to real time, it means that the forms of the virus circulating today are only about 15 accumulated mutations or so, different from the first version traced to the outbreak in Wuhan in China. This really is a tiny number when one considers the fact that the SARS-CoV-2 genome consists of about 30,000 nucleotide components. The implication is that the viral versions that are prevalent today are at least 99.9 per cent the same as the original index strain from Wuhan. If one were to say it in a more simplified way, for an RNA virus, SARS-CoV-2 is in the slowest lane of evolution.
In fact, from a purely scientific perspective, all these discussions of SARS-CoV-2 having developed into however many different “strains” is misleading. Scientists tend to reserve the word ‘strain’ for versions of a virus that differs from the original in major biological ways. SARS-CoV-2’s different forms are very similar; and technically, it is far better to label them as “variants”.
The coronavirus’s sluggish pace of mutation is good news for us. That is because a virus that evolved more rapidly would have a greater chance of outrunning any vaccines or drugs developed to counter it. Having said that, have even the small mutations so far changed SARS-CoV-2 in any important ways? For example, has it become more deadly? The answer might surprise many. Up to the present time, there is no evidence to suggest that any newer or mutated forms of SARS-CoV-2 have become more virulent or more lethal; nor for that matter, that it has become less so as well.
For example, a recent preprint paper (i.e. not yet peer-reviewed) by Erik Volz, of Imperial College, London, UK, and other co-workers, including members of the Covid-19 Genomics UK Consortium which analysed 25,000 whole genome SARS-CoV-2 sequences collected in the United Kingdom, found that one particular mutation in the virus, known as D614G, had not increased mortality in patients. There has been much discussion over whether the D614G mutation, which affects the so-called spike protein of the virus, has made SARS-CoV-2 more infectious. In a very broad sense this appears to be so and that contention has led to some of the affected countries to which it has spread, taking drastic steps in locking-down certain areas.
The spike protein sits on the surface of the coronavirus, and that really matters because it’s the part of the virus that attaches itself to the host’s cells. “D614G” is an abbreviation for a change at position 614 of the spike protein. The D614G mutation, which probably initially arose in China, first appeared to become more and more frequent in the outbreak in northern Italy in February. The G614 form of the virus has since spread all over the world and has become the dominant variant. The D614G mutation does seem to have increased the infectivity of the coronavirus, at least in cells grown in laboratories, according to a recent paper by the computational biologist Bette Korber and others, published in the journal ‘Cell’. Apparently based partly on this and some other studies as well, health authorities in various countries have claimed that the G614 form of the coronavirus may be 10 times more infectious than the version first detected in Wuhan.
The more recent UK variant, commonly known as B-1.1.7, is definitely a more contagious variant of the coronavirus. It first emerged in the U.K. in late 2020. It has 23 accumulated mutations. It has acquired 17 of these at once, a feat that has not been seen before. Of particular concern to scientists are eight mutations that affect the gene for a spike protein on the surface of coronaviruses. The worries are the results of the fact that the viruses use the spike protein to grab onto human cells. This mutant strain too appeared to spread faster than other variants in the United Kingdom but has not shown itself to cause more severe disease.
These scientific details could have an abiding effect on the future of this capricious and miserable virus that causes COVID-19. A pandemic virus may disappear from the scene due to one or more of three reasons. The first of these is the notion that a virus that is capable of taking lives would kill a significant number of affected people but those who manage to recover will have some degree of immunity against the very same virus. So, reinfections may be naturally prevented following the first infection with the virus, provided of course that the patient survives the initial onslaught. The second factor is that the virus may induce extensive immunity in a populace, the so-called ‘herd immunity’, either through widespread infection of a large proportion of the population or a similar scenario being enacted through vaccination against the virus. The end result of this is to produce a rather resistant population against the effects of the virus. The third possibility is that repeated mutations would lead to converting the virus into a much less troublesome and less virulent form that it ceases to be a major medical problem and converts the blight into an insignificant and toothless type of an entity. Such impotent strains might even be able to completely overwhelm the more virulent types, with tremendously beneficial implications for the whole of humanity.
These are thought to be at least some of the mechanisms through which the Spanish Flu of 1918 disappeared within a year or so. It was destined never to return in the same life-threatening format for a period of over 100 years or so, right up to the present time.
It has been said that hope springs eternal in the human breast. We do hope and even pray that through some of these postulated mechanisms, the inhabitants of Mother Earth would be spared further turmoil, intense suffering and absolute mayhem that has been their lot for the last year or so, through the doings of this dastardly blight of a nasty coronavirus. We have suffered immeasurably. It is about time that we got a decent break in this fight.
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There’s an ill more dangerous and pervasive than the Coronavirus that’s currently sweeping Sri Lanka. That is the fear to express one’s convictions. Across the public sector of the country in particular many persons holding high office are stringently regulating and controlling the voices of their consciences and this bodes ill for all and the country.
The corrupting impact of fear was discussed in this column a couple of weeks ago when dealing with the military coup in Myanmar. It stands to the enduring credit of ousted Myanmarese Head of Government Aung San Suu Kyi that she, perhaps for the first time in the history of modern political thought, singled out fear, and not power, as the principal cause of corruption within the individual; powerful or otherwise.
To be sure, power corrupts but the corrupting impact of fear is graver and more devastating. For instance, the fear in a person holding ministerial office or in a senior public sector official, that he would lose position and power as a result of speaking out his convictions and sincere beliefs on matters of the first importance, would lead to a country’s ills going unaddressed and uncorrected.
Besides, the individual concerned would be devaluing himself in the eyes of all irrevocably and revealing himself to be a person who would be willing to compromise his moral integrity for petty worldly gain or a ‘mess of pottage’. This happens all the while in Lankan public life. Some of those who have wielded and are wielding immense power in Sri Lanka leave very much to be desired from these standards.
It could be said that fear has prevented Sri Lanka from growing in every vital respect over the decades and has earned for itself the notoriety of being a directionless country.
All these ills and more are contained in the current controversy in Sri Lanka over the disposal of the bodies of Covid victims, for example. The Sri Lankan polity has no choice but to abide by scientific advice on this question. Since authorities of the standing of even the WHO have declared that the burial of the bodies of those dying of Covid could not prove to be injurious to the wider public, the Sri Lankan health authorities could go ahead and sanction the burying of the bodies concerned. What’s preventing the local authorities from taking this course since they claim to be on the side of science? Who or what are they fearing? This is the issue that’s crying out to be probed and answered.
Considering the need for absolute truthfulness and honesty on the part of all relevant persons and quarters in matters such as these, the latter have no choice but to resign from their positions if they are prevented from following the dictates of their consciences. If they are firmly convinced that burials could bring no harm, they are obliged to take up the position that burials should be allowed.
If any ‘higher authority’ is preventing them from allowing burials, our ministers and officials are conscience-bound to renounce their positions in protest, rather than behave compromisingly and engage in ‘double think’ and ‘double talk’. By adopting the latter course they are helping none but keeping the country in a state of chronic uncertainty, which is a handy recipe for social instabiliy and division.
In the Sri Lankan context, the failure on the part of the quarters that matter to follow scientific advice on the burials question could result in the aggravation of Islamophobia, or hatred of the practitioners of Islam, in the country. Sri Lanka could do without this latter phobia and hatred on account of its implications for national stability and development. The 30 year war against separatist forces was all about the prevention by military means of ‘nation-breaking’. The disastrous results for Sri Lanka from this war are continuing to weigh it down and are part of the international offensive against Sri Lanka in the UNHCR.
However, Islamophobia is an almost world wide phenomenon. It was greatly strengthened during Donald Trump’s presidential tenure in the US. While in office Trump resorted to the divisive ruling strategy of quite a few populist authoritarian rulers of the South. Essentially, the manoeuvre is to divide and rule by pandering to the racial prejudices of majority communities.
It has happened continually in Sri Lanka. In the initial post-independence years and for several decades after, it was a case of some populist politicians of the South whipping-up anti-Tamil sentiments. Some Tamil politicians did likewise in respect of the majority community. No doubt, both such quarters have done Sri Lanka immeasurable harm. By failing to follow scientific advice on the burial question and by not doing what is right, Sri Lanka’s current authorities are opening themselves to the charge that they are pandering to religious extremists among the majority community.
The murderous, destructive course of action adopted by some extremist sections among Muslim communities world wide, including of course Sri Lanka, has not earned the condemnation it deserves from moderate Muslims who make-up the preponderant majority in the Muslim community. It is up to moderate opinion in the latter collectivity to come out more strongly and persuasively against religious extremists in their midst. It will prove to have a cementing and unifying impact among communities.
It is not sufficiently appreciated by governments in the global South in particular that by voicing for religious and racial unity and by working consistently towards it, they would be strengthening democratic development, which is an essential condition for a country’s growth in all senses.
A ‘divided house’ is doomed to fall; this is the lesson of history. ‘National security’ cannot be had without human security and peaceful living among communities is central to the latter. There cannot be any ‘double talk’ or ‘politically correct’ opinions on this question. Truth and falsehood are the only valid categories of thought and speech.
Those in authority everywhere claiming to be democratic need to adopt a scientific outlook on this issue as well. Studies conducted on plural societies in South Asia, for example, reveal that the promotion of friendly, cordial ties among communities invariably brings about healing among estranged groups and produces social peace. This is the truth that is waiting to be acted upon.
Author
By Sanjeewa Jayaweera
It was on 3rd January 1972 that our family arrived in Karachi from Moscow. Our departure from Moscow had been delayed for a few weeks due to the military confrontation between Pakistan and India. It ended on 16th December 1971. After that, international flights were not permitted for some time.
The contrast between Moscow and Karachi was unbelievable. First and foremost, Moscow’s temperature was near minus 40 degrees centigrade, while in Karachi, it was sunny and a warm 28 degrees centigrade. However, what struck us most was the extreme warmth with which the airport authorities greeted our family. As my father was a diplomat, we were quickly ushered to the airport’s VIP Lounge. We were in transit on our way to Rawalpindi, the airport serving the capital of Islamabad.
We quickly realized that the word “we are from Sri Lanka” opened all doors just as saying “open sesame” gained entry to Aladdin’s cave! The broad smile, extreme courtesy, and genuine warmth we received from the Pakistani people were unbelievable.
This was all to do with Mrs Sirima Bandaranaike’s decision to allow Pakistani aircraft to land in Colombo to refuel on the way to Dhaka in East Pakistan during the military confrontation between Pakistan and India. It was a brave decision by Mrs Bandaranaike (Mrs B), and the successive governments and Sri Lanka people are still enjoying the fruits of it. Pakistan has been a steadfast and loyal supporter of our country. They have come to our assistance time and again in times of great need when many have turned their back on us. They have indeed been an “all-weather” friend of our country.
Getting back to 1972, I was an early beneficiary of Pakistani people’s love for Sri Lankans. I failed the entrance exam to gain entry to the only English medium school in Islamabad! However, when I met the Principal, along with my father, he said, “Sanjeewa, although you failed the entrance exam, I will this time make an exception as Sri Lankans are our dear friends.” After that, the joke around the family dinner table was that I owed my education in Pakistan to Mrs B!
At school, my brother and I were extended a warm welcome and always greeted “our good friends from Sri Lanka.” I felt when playing cricket for our college; our runs were cheered more loudly than of others.
One particular incident that I remember well was when the Embassy received a telex from the Foreign inistry. It requested that our High Commissioner seek an immediate meeting with the Prime Minister of Pakistan, Mr Zulifikar Ali Bhutto (ZB), and convey a message from Mrs B. The message requested that an urgent shipment of rice be dispatched to Sri Lanka as there would be an imminent rice shortage. As the Ambassador was not in the station, the responsibility devolved on my father.
It usually takes about a week or more to get an audience with the Prime Minister (PM) of a foreign country due to their busy schedule. However, given the urgency, my father spoke to the Foreign Ministry’s Permanent Sectary, who fortunately was our neighbour and sought an urgent appointment. My father received a call from the PM’s secretary around 10 P.M asking him to come over to the PM’s residence. My father met ZB around midnight. ZB was about to retire to bed and, as such, was in his pyjamas and gown enjoying a cigar! He had greeted my father and had asked, “Mr Jayaweera, what can we do for great friend Madam Bandaranaike?. My father conveyed the message from Colombo and quietly mentioned that there would be riots in the country if there is no rice!
ZB had immediately got the Food Commissioner of Pakistan on the line and said, “I want a shipload of rice to be in Colombo within the next 72 hours!” The Food Commissioner reverted within a few minutes, saying that nothing was available and the last export shipment had left the port only a few hours ago to another country. ZB had instructed to turn the ship around and send it to Colombo. This despite protests from the Food Commissioner about terms and conditions of the Letter of Credit prohibiting non-delivery. Sri Lanka got its delivery of rice!
The next was the visit of Mrs B to Pakistan. On arrival in Rawalpindi airport, she was given a hero’s welcome, which Pakistan had previously only offered to President Gaddafi of Libya, who financially backed Pakistan with his oil money. That day, I missed school and accompanied my parents to the airport. On our way, we witnessed thousands of people had gathered by the roadside to welcome Mrs B.
When we walked to the airport’s tarmac, thousands of people were standing in temporary stands waving Sri Lanka and Pakistan flags and chanting “Sri Lanka Pakistan Zindabad.” The noise emanating from the crowd was as loud and passionate as the cheering that the Pakistani cricket team received during a test match. It was electric!
I believe she was only the second head of state given the privilege of addressing both assemblies of Parliament. The other being Gaddafi. There was genuine affection from Mrs B amongst the people of Pakistan.
I always remember the indefatigable efforts of Mr Abdul Haffez Kardar, a cabinet minister and the President of the Pakistan Cricket Board. From around 1973 onwards, he passionately championed Sri Lanka’s cause to be admitted as a full member of the International Cricket Council (ICC) and granted test status. Every year, he would propose at the ICC’s annual meeting, but England and Australia’s veto kept us out until 1981.
I always felt that our Cricket Board made a mistake by not inviting Pakistan to play our inaugural test match. We should have appreciated Mr Kardar and Pakistan’s efforts. In 1974 the Pakistan board invited our team for a tour involving three test matches and a few first-class games. Most of those who played in our first test match was part of that tour, and no doubt gained significant exposure playing against a highly talented Pakistani team.
Several Pakistani greats were part of the Pakistan and India team that played a match soon after the Central Bank bomb in Colombo to prove that it was safe to play cricket in Colombo. It was a magnificent gesture by both Pakistan and India. Our greatest cricket triumph was in Pakistan when we won the World Cup in 1996. I am sure the players and those who watched the match on TV will remember the passionate support our team received that night from the Pakistani crowd. It was like playing at home!
I also recall reading about how the Pakistani government air freighted several Multi Barrell artillery guns and ammunition to Sri Lanka when the A rmy camp in Jaffna was under severe threat from the LTTE. This was even more important than the shipload of rice that ZB sent. This was crucial as most other countries refused to sell arms to our country during the war.
Time and again, Pakistan has steadfastly supported our country’s cause at the UNHCR. No doubt this year, too, their diplomats will work tirelessly to assist our country.
We extend a warm welcome to Mr Imran Khan, the Prime Minister of Pakistan. He is a truly inspirational individual who was undoubtedly an excellent cricketer. Since retirement from cricket, he has decided to get involved in politics, and after several years of patiently building up his support base, he won the last parliamentary elections. I hope that just as much as he galvanized Sri Lankan cricketers, his political journey would act as a catalyst for people like Kumar Sangakkara and Mahela Jayawardene to get involved in politics. Cricket has been called a “gentleman’s game.” Whilst politics is far from it!.
Author
Believe me, seeing certain videos, on social media, depicting action, on the dance floor, at some of these entertainment venues, got me wondering whether this Coronavirus pandemic is REAL!
To those having a good time, at these particular venues, and, I guess, the management, as well, what the world is experiencing now doesn’t seem to be their concerned.
Obviously, such irresponsible behaviour could create more problems for those who are battling to halt the spread of Covid-19, and the new viriant of Covid, in our part of the world.
The videos, on display, on social media, show certain venues, packed to capacity – with hardly anyone wearing a mask, and social distancing…only a dream..
How can one think of social distancing while gyrating, on a dance floor, that is over crowded!
If this trend continues, it wouldn’t be a surprise if Coronavirus makes its presence felt…at such venues.
And, then, what happens to the entertainment scene, and those involved in this field, especially the musicians? No work, whatsoever!
Lots of countries have closed nightclubs, and venues, where people gather, in order to curtail the spread of this deadly virus that has already claimed the lives of thousands.
Thailand did it and the country is still having lots of restrictions, where entertainment is concerned, and that is probably the reason why Thailand has been able to control the spread of the Coronavirus.
With a population of over 69 million, they have had (so far), a little over 25,000 cases, and 83 deaths, while we, with a population of around 21 million, have over 80,000 cases, and more than 450 deaths.
I’m not saying we should do away with entertainment – totally – but we need to follow a format, connected with the ‘new normal,’ where masks and social distancing are mandatory requirements at these venues. And, dancing, I believe, should be banned, at least temporarily, as one can’t maintain the required social distance, while on the dance floor, especially after drinks.
Police spokesman DIG Ajith Rohana keeps emphasising, on TV, radio, and in the newspapers, the need to adhere to the health regulations, now in force, and that those who fail to do so would be penalised.
He has also stated that plainclothes officers would move around to apprehend such offenders.
Perhaps, he should instruct his officers to pay surprise visits to some of these entertainment venues.
He would certainly have more than a bus load of offenders to be whisked off for PCR/Rapid Antigen tests!
I need to quote what Dr. H.T. Wickremasinghe said in his article, published in The Island of Tuesday, February 16th, 2021:
“…let me conclude, while emphasising the need to continue our general public health measures, such as wearing masks, social distancing, and avoiding crowded gatherings, to reduce the risk of contact with an infected person.
“There is no science to beat common sense.”
But…do some of our folks have this thing called COMMON SENSE!
