We have probably not seen the last of the mutations and variants of the Covid-19 virus. Perhaps the world got a lucky break with Omicron. Perhaps not
By Anil Madan
The latest hot topic in the seemingly never-ending saga of the Covid-19 pandemic is the emergence of the latest variant known as Omicron. Although new information comes to light every day, much remains unknown.
South Africa was the first country to report on November 24, the detection of a new variant of the SARS-CoV-2 (or Covid-19) virus to the World Health Organization (WHO) which gave it the designation “Omicron.” The WHO which has been using letters of the Greek alphabet to designate variants of the virus, later explained that it skipped the Greek letters Nu and Chi or Xi that would have been next in line had it followed the alphabet in sequence because the Greek letter Nu could have been confused with “new” and because Xi is the name of you know who. No, it certainly would have been unseemly to name what has already been called a “novel” coronavirus a “Nu novel” virus or to call a virus that originated in Wuhan, the Xi virus. Who knew?
Omicron. Pic – AFP
Following the report that this variant was spreading rapidly in southern African countries, President Biden imposed a travel ban from eight African countries. Soon, Canada, Britain and European countries followed suit with travel bans of their own.
President Joe Biden explained his decision to restrict travel from countries in southern Africa applied to countries that have seen “significant” numbers of cases of the omicron variant. However, he conceded that the restrictions will not stop the variant from coming into the United States but would slow it down and his approach would give people who have not had the booster shot of the Covid-19 vaccination, as well as those who have not been vaccinated at all, time to get a shot. President Biden acknowledged that it would take at least a couple of weeks for scientists to figure out how deadly the Omicron variant is, how transmissible it is and whether existing vaccines are effective against it.
The travel bans were met with loud protests from President Cyril Ramaphosa of South Africa and in a written opinion by the Chair of the South African Medical Association, Dr Angelique Coetzee. Their complaints amount principally to assertions that the travel bans are arbitrary and unfair and that South Africa is being punished for being responsible about reporting the detection of the Omicron variant. Others have chimed in with laments about inequities in the worldwide distribution of vaccines and some have even called the bans a new form of apartheid. The last claim is easily dismissed since the US has in the past imposed travel bans on Canada as well as European countries.
Dr Coetzee’s lament is, in my view, illogical, filled with contradictions.
First, she claims that she announced the presence of the Omicron variant in one of her patients due to her public-facing role. But she also asserts that “We’ve become accustomed here to new Covid variants emerging,” meaning in South Africa, and when South African scientists confirmed the discovery of another, no one made a huge thing of it and many didn’t even notice. But it is fair to ask why she reported what she now downplays. To her credit, her reporting was probably based on the fact that she noticed that this particular variant had significantly more mutations than previous variants and, in this case, about the spike protein as well as elsewhere in the virus structure. Saying that no one made a huge thing of it and many didn’t even notice seems disingenuous. Indeed, South Africa continues to track and report surging infections with this variant.
Second, she says we don’t know anywhere near enough about Omicron to make judgments about flight bans, masking and quarantines. But that is precisely the problem. The entire purpose of early reporting of outbreaks is to allow imposition of preventive measures while we try to gather information. The failures to take early and decisive action against the original outbreaks of Covid-19 in 2020 and perhaps as early as 2019, should not be repeated.
Third, on the subject of gathering information, she offers only anecdotal evidence of mild cases in her first patient and five others she has since seen. Missing entirely from her commentary is any mention of the surge in cases in South Africa—in fairness, she probably wrote the piece before the latest numbers were announced. However, shortly after Dr Coetzee wrote her opinion piece, it was reported that cases in South Africa surged to some 8,500 almost double the previous day’s 4,300 and the country’s institute of communicable diseases reported that more than 70% of all virus genome variants sequenced in the last month have been of the Omicron variety. See Omicron drives major surge in S. Africa Covid cases (msn.com).
Since then, the numbers have increased astronomically. Last Friday, South Africa’s National Institute for Communicable Diseases (NICD) reported: “Today the institute reports 16,055 new Covid-19 cases that have been identified in South Africa… This increase represents a 24.3% positivity rate.” On Thursday, the NICD also revealed that some of the new cases were people who had previously had Covid-19 and had been reinfected with the Omicron variant. The variant appears to be highly transmissible.
The charges of inequities in vaccine distribution come not only from some South Africans but also from the top levels of the WHO. But these too are, in context, misplaced. While there is no question that the richer western nations have more plentiful and easier access to vaccines, this is hardly the result of a sinister plot to deprive African nations and other poor countries of vaccines.
The New York Times reported recently that just days before scientists discovered the Omicron variant, South Africa’s government asked Johnson & Johnson and Pfizer not to make some planned deliveries of their Covid-19 vaccines. The country already had more doses in storage than it could use — about 16 million, in a country of 60 million people — and officials were worried that further supplies would spoil before they could be used. The NYT went on to describe vaccine skepticism and vaccine hesitancy in South Africa as major factors leading to such situations.
The WHO set a target of trying to get at least 40% of the world’s population vaccinated by the end of 2021. That means vaccinating 3 billion people. If the WHO’s goal was two shots per person, that would mean a total of 6 billion doses; if one shot, it would mean 3 billion doses of a one-shot vaccine. We know that the world simply did not have that much production capacity at the beginning of 2021. Going forward, there is likely to be a significant ramp up of vaccine production and the WHO’s goals may be met and exceeded in 2022. But the key is that vaccinating 40% of the world’s population is not the panacea that would have stopped Omicron. Nor would meeting such a goal stop the evolution of future variants. But there is no question that a more concerted effort to vaccinate frontline healthcare workers in Africa is a priority.
The Omicron variant has the greatest number of mutations yet seen in the SARS-CoV-2 virus that causes Covid-19. It has 50 mutations in total, with 32 mutations on the spike protein. The spike protein often depicted graphically as protrusions extending outward from the virus, allows the virus to latch on to human cells which allows it to enter the cell and replicate. The good news is that this same spike protein is used by the three major vaccines available in the US (Pfizer, Moderna, and J&J) and presumably by other vaccines to trigger the production of antibodies.
Whereas the extensive mutations found in Omicron could make it more contagious or worse yet, more able to evade antibodies, the presence of a common target spike protein also suggests that the vaccines will continue to be effective. The Chairman of Moderna offered during a recent television appearance that the vaccine dosing might be increased to give greater protection against Omicron, or a more specific vaccine targeted at Omicron could be tweaked and ready within a few months.
So far, people infected with the Omicron variant have presented with mild symptoms and no deaths have been reported. The Delta variant has been the predominant mutation causing infections in the US and presumably in Europe and most of the world. If the Omicron variant can beat out all other existing virus variants and supplant the Delta variant, the possible plus is that SARS-CoV2 may have been reduced to a milder virus. At this point, it is too early to say.
It is difficult to criticize the Biden administration for taking preventive measures such as a travel ban. But, in truth, the travel ban was probably too late. By the time the existence of the virus was reported, it had probably already travelled across the world. Recent reports of infections in the US, Canada, Britain and in some European countries confirm this. On the other hand, curbing travel may have reduced the extent of transmission of the virus.
The US Centers for Disease Control and Prevention (CDC) notes that viruses like SARS-CoV-2, what we commonly refer to as Covid-19, continuously evolve as changes in the genetic code (genetic mutations) occur during replication of the genome. Replication occurs when people are infected and the virus makes copies of itself. A variant has one or more mutations that differentiate it from other variants of the SARS-CoV-2 viruses. And as the CDC notes, we are all aware that multiple variants of SARS-CoV-2 have been documented in the United States and globally throughout this pandemic. In fact, scientists have been warning since the beginning of this pandemic that until the virus is brought under control by having people around the world vaccinated, the danger of mutations that may be resistant to existing vaccines remains an ever-present possibility.
The CDC keeps track of viruses by lineage, mutation, and variant. The CDC states that a lineage is a group of closely related viruses, with a common ancestor. SARS-CoV-2 has many lineages; all cause Covid-19.
The lesson is that we have probably not seen the last of the mutations and variants of the Covid-19 virus. Perhaps the world got a lucky break with Omicron. Perhaps not. If the former, this tragedy may have a lighter ending. If the latter, a full-fledged Greek tragedy continues.
* Published in print edition on 7 December 2021
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